Abstract

The Rising Star cave system has produced abundant fossil hominin remains within the Dinaledi Chamber, representing a minimum of 15 individuals attributed to Homo naledi. Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi. Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi, and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species.

eLife digest

Species of ancient humans and the extinct relatives of our ancestors are typically described from a limited number of fossils. However, this was not the case with Homo naledi. More than 1500 fossils representing at least 15 individuals of this species were unearthed from the Rising Star cave system in South Africa between 2013 and 2014. Found deep underground in the Dinaledi Chamber, the H. naledi fossils are the largest collection of a single species of an ancient human-relative discovered in Africa.

After the discovery was reported, a number of questions still remained. These questions included: why were so many fossils from a single species found at the one site, and how did they come to rest so far into the cave system? Possible explanations such as H. naledi living in the cave or being washed in by a flood were considered but ruled out. Instead, the evidence was largely consistent with intact bodies being deliberately disposed of in the cave and then decomposing.

Now, Hawks et al. – who include many of the researchers who were involved in the discovery of H. naledi – report that yet more H. naledi fossils have been unearthed from a second chamber in the Rising Star cave system, the Lesedi Chamber. The chamber is 30 meters below the surface and there is no direct route between it and the Dinaledi Chamber. Again, the evidence is most consistent with the bodies arriving intact into the chamber, and there were no signs that the remains had been exposed to the surface environment.

Also like the Dinaledi Chamber, no remains of other ancient humans or their relatives were found in the Lesedi Chamber. In total, 133 fossils of H. naledi have been found in this second chamber representing at least three individuals: two adults and a juvenile. However, and as Hawks et al. point out, only a small volume of the chamber has been excavated so far, and so there are likely more fossils still to be found.

The fossils in the Lesedi Chamber are similar to those found before but include intact examples of bones, like the collarbone, that were previously known only from fragments. Perhaps the most impressive among the new fossils is a relatively complete skull that is part of a partial skeleton. The skull could have housed a brain that was 9% larger than the maximum estimate calculated from the previous H. naledi fossils.

Though these new fossils provide us with yet more information about H. naledi, some questions still remain unanswered – the material from the Lesedi Chamber is undated, for example. However, a related study by Dirks et al. does give an estimate for the age of the fossils from the Dinaledi Chamber, while Berger et al. provide an explanation for why this date might be much younger than was previously predicted.

Introduction

The Rising Star cave system (26°1′13′′ S; 27°42′43′′ E, Figure 1) in the Cradle of Humankind World Heritage Site, Gauteng Province, South Africa, is known for the discovery in 2013 of more than 1,550 fossils representing a novel hominin species, Homo naledi (Berger et al., 2015; Dirks et al., 2015). These remains, representing at least 15 individuals of various ages at death, were recovered from a deep chamber (30 m below ground surface), named the Dinaledi Chamber.

Geographical location of the Rising Star cave in the Cradle of Humankind UNESCO World Heritage Site.

Additional fossil hominin material was subsequently discovered in the Lesedi Chamber of the cave system in November 2013 by Rick Hunter and Steven Tucker. The deposition of sediment and skeletal remains in the Lesedi Chamber has no direct geological connection to the Dinaledi Chamber. In the time following the first discovery of hominin material in the Lesedi Chamber, excavators have recovered 131 hominin specimens within three discrete collection areas. The sedimentary context of the three collection areas is broadly similar, but we have not yet established whether the fossil material resulted from a single depositional episode or from multiple distinct events.

We approached the hominin skeletal remains from the Lesedi Chamber with the aim of identifying elements, assessing the number of individuals represented by the material, and determining the taxonomic identity of the sample. Preliminary examination of the hominin remains suggested that they are morphologically consistent with H. naledi. To test this hypothesis, we carried out systematic comparisons, employing the taxonomic diagnosis of this species (Berger et al., 2015) and focusing upon those characters that distinguish H. naledi from other hominin taxa. We also present essential contextual information to place the specimens within the Lesedi Chamber and provide descriptions of the hominin specimens, focusing upon those features that contribute to the taxonomic diagnosis of the sample. All identifiable hominin fragments, including those that do not present information useful to taxonomic diagnosis, are listed in Table 1.

Table 1

Hominin fossil material from the Lesedi Chamber. All diagnostic hominin specimens are listed, with attribution to element. Specimens that have been refitted are not listed separately. Most Locality 102a cranial fragments are presumed to be part of LES1 and are not listed separately.

Results

Name of the chamber

Following the University of the Witwatersrand’s fossil-numbering system (Zipfel and Berger, 2009), this second H. naledi locality has been designated U.W. 102. The chamber itself has been named the Lesedi Chamber, a word meaning ‘light’ in Setswana. By contrast, the Dinaledi Chamber was numbered site U.W. 101. Excavations in the Lesedi Chamber have been carried out in three areas, designated U.W. 102a, U.W. 102b, and U.W. 102c.

Location of the Lesedi Chamber

The Lesedi Chamber is in the central sector of the Rising Star system (Figure 2), at a depth of ~30 m from the surface directly above the chamber. All measurements reported here are approximate. The first fossil deposit to be recognized (U.W. 102a) is located just off the southwest corner of the North-South Fracture Passage, a northern arm of the Lesedi Chamber. This fossil deposit is approximately 60 m NNE in a straight line from the Dinaledi Chamber. There is no straight-line route between the Dinaledi and Lesedi Chambers, and the shortest traversable route between the two areas is almost 145 m. There are currently four access routes from the surface to the Lesedi Chamber. The most accessible of these currently follows an 86 m downward-sloping path with several narrow passages and short climbs, but only one squeeze and no significant crawls. This has been the main access route for excavators. The other three routes are each substantially more challenging.

Location of the Lesedi Chamber (U.W.102) in the Rising Star system (red circle).

Location of skeletal material within the Lesedi Chamber

In addition to the first fossil deposit to be recognized in the chamber, two additional concentrations of skeletal material have been identified to date (Figure 3), and we have designated these as areas 102a, 102b, and 102c. We began investigating each of these areas because team members noticed hominin fossil material exposed on sediment surfaces. The discovery of 102a by Rick Hunter and Steven Tucker led to the initial scientific investigation of the chamber; discoveries of both 102b and 102c were made by Hannah Hilbert-Wolf during the course of geological sampling of the chamber. These three areas do not represent a systematic sampling of the chamber’s contents and we have excavated only a very small sediment volume, less than 200 L (<0.2 m3) in total from all three areas. The chamber contains a much greater volume of sediment and we do not know what density of fossil bone it may contain beyond our samples.

Schematic of the Lesedi Chamber, showing the three hominin-bearing collection areas: U.W.102a, 102b, and 102c.

U.W. 102a is located at the entrance of a 20–50-cm-wide blind tunnel, which is 1.8 m long in total. The blind tunnel leads off of the southwest corner of the North-South Fracture Passage (Figure 3). Fossil material was exposed on the surface within this blind tunnel at the time of discovery. We have excavated the proximal 1.5 m of this blind tunnel, which has a tapering width of less than 50 cm in our excavation unit. The depth of excavation in this area is a maximum of 40 cm. The deposit in this area is a weakly stratified, unlithified mud-clast breccia. Most hominin material has been recovered from an approximately 10-cm-thick horizon of fine-grained mud-clast breccia, beneath a surface layer of ~2 cm of lighter brown-colored mudstone. This deposit is the source of at least some of the sediments that slope from the blind tunnel into the Antechamber. Fossil material attributed to 102a has also been recovered from the surface within the North-South Fracture Passage.

U.W. 102b is a sediment deposit on a horizontal chert shelf 80 cm above the cave floor along the western wall of the Antechamber. It is also dominated by unlithified mud-clast breccia. The 102b deposit is located ~3.8 m to the south and 1.8 m below the 102a deposit. After the discovery of hominin fossil material on the surface here, we undertook limited excavations, with a total volume of ~20 L.

U.W. 102c is a small unlithified sediment deposit within an irregular dissolution cavity on the north wall of the east–west-running Cake-Icing Fracture. This deposit is 1.3 m above the current cave floor. It is 11.6 m from U.W. 102a, and 0.3 m below the level of the 102a fossils. We have excavated this small sediment pocket in its entirely, with a total volume of approximately 2 L.

Geological work to characterize the Lesedi Chamber depositional history is underway. The stratigraphy is complex, with some hominin and faunal material concentrated in deposits of poorly consolidated mud-clast breccia, generally similar to the facies in the Dinaledi Chamber (Dirks et al., 2015). Notably, the fossil material in the Lesedi Chamber is concentrated in minor side fractures, dissolution cavities, or on chert shelves well above the current chamber floor. Our working hypothesis is that the chamber once held a greater volume of sediment than is present today, and when sediment eroded from the chamber, erosional remnants remained in protected fractures, wall cavities, and on chert shelves along the chamber walls. This and other indications of reworking of the deposits make it uncertain how much of the hominin assemblage may remain in its primary depositional context.

Hominin material from 102a

Hominin material from the 102a area includes 118 identifiable specimens (Table 1; Figure 4). Fifty-seven of these are cranial and dental specimens that either refit directly or are morphologically compatible with a nearly complete fossil cranium, designated LES1 (Figure 5). Hominin postcranial remains from locality 102a include 61 identified specimens that represent a minimum of 31 postcranial elements, not counting ribs. These include a minimum of two partial femora, two partial humeri, one complete clavicle and two clavicular fragments, two partial ulnae, several fragments of scapula and radius, many rib fragments, a near-complete first rib, a partial sternum, four hand and wrist elements, an immature ilium and sacrum fragment, and a partial thoracic and lumbar vertebral column. Every anatomical region of the skeleton is represented with the notable exceptions of tibia, fibula and pedal remains.

The adult cranial material from 102a all belongs to a single cranium; most of the adult postcranial material probably belongs to the same individual. The adult cranial and postcranial material is shown here, except for the U.W. 102a-001 femur. The possibility that the femora represent two adult individuals makes it unclear which femur may be attributable to the skeleton; for the purposes of illustration, the U.W. 102a-003/U.W. 102a-004 femur is included in this photograph.

LES1 cranium.

Clockwise from upper left: three-quarter, frontal, superior and left lateral views. Fragments of the right temporal, the parietal and the occipital have also been recovered (not pictured), but without conjoins to the reconstructed vault or face. Scale bar = 5 cm.

LES1

The LES1 cranium is fragmented but is represented by most of the vault and part of the face (Figure 5). To date, we have successfully refitted the near-complete mandible, the near-complete right maxilla, a partial palate and a partial left maxillary dental row, and a partial vault including the near-complete frontal, left and right nasal and left lacrimal bones, near-complete left parietal and temporal, partial right parietal, and a portion of left occipital. LES1 has a complete adult dentition except for the crowns of the lower left central and lateral incisors. The face is reconstructed from the partial right maxillary bone, including the frontal process, which refits to the right nasal bone and frontal. The left mandibular ramus is well-enough preserved to allow a rough estimation of the condyle position, enabling an approximation of the midsagittal contour of the face (Figure 5).

All additional cranial fragments in the present 102a collection are non-duplicative with this refitted vault and face, and where they represent the opposite side of the vault, they match in morphological detail. However, many of the fragments lack clear refits with the existing vault or maxillary portions. Further physical reconstruction of the cranium will await fragments that may emerge from excavation in the future. The refitted vault, with the application of virtual mirror reconstruction, is sufficient to allow an estimate of endocranial volume of approximately 610 ml (Figure 6).

Digital reconstruction of endocranial volume in LES1.

Most of the features of the LES1 vault are characteristic of H. naledi from the Dinaledi Chamber (Supplementary file 1; Figure 7). The LES1 vault is relatively short anteroposteriorly, without the elongation and sharp occipital angulation found in H. erectus. LES1 exhibits mild frontal and parietal bossing, similar to H. naledi DH3. Other features on the vault that are consistent with H. naledi include prelambdoidal flattening, limited postorbital constriction, widely spaced temporal lines, a continuous supraorbital torus with a supratoral sulcus, an occipital torus, and a marked angular torus. In the temporal region, LES1 has an anteroinferiorly oriented root of the zygomatic process of the temporal, a medially positioned mandibular fossa, a small and obliquely oriented external auditory meatus, a projecting Eustachian process, a small vaginal process, a weak crista petrosa, a triangular-shaped mastoid process, and a small suprameatal spine. Each of these traits characterizes the Dinaledi H. naledi sample (Berger et al., 2015; Laird et al., 2017). Some of these traits occur individually in other species, including H. erectus, H. habilis, H. rudolfensis, and Australopithecus sediba, but they have never been found in combination except in H. naledi (Figure 7).

Frontal and vault morphology in H. naledi compared to that in other hominin species.

Several of the crania pictured here are similar to H. naledi in endocranial volume, including Sts 5, MH1, KNM-ER 1813, and D2282, representing four different species. However, these skulls contrast strongly in other features. H. erectus is highly variable in size, as illustrated here by D2282 from Dmanisi, Georgia, one of the smallest and earliest H. erectus crania, and the L2 cranium from Zhoukoudian, China, one of the largest and latest H. erectus specimens. The relatively early KNM-ER 3733 has a size and endocranial volume close to the mean for H. erectus. Cranial remains that are attributed to H. erectus share a combination of anatomical features despite their diversity in size. Many such features of H. erectus are also shared with H. naledi, H. habilis, or Au. sediba, and notably, the differences in the frontal and vault between KNM-ER 1813 (H. habilis) and KNM-ER 1470 (H. rudolfensis) are mostly features that the smaller KNM-ER 1813 shares with H. naledi, H. erectus, and Au. sediba. The H. naledi skulls share some aspects of frontal morphology with Au. sediba, H. habilis and H. erectus that are not found in Au. africanus or H. rudolfensis, including frontal bossing and a supratoral sulcus. Two additional traits of the H. naledi anterior vault are shared with Au. sediba and H. erectus:slight postorbital construction and a posterior position of the temporal crest on the supraorbital torus. More posteriorly on the vault, H. naledi further shares an angular torus with H. erectus, and some individuals also have sagittal keeling. Both of these traits are also present in some archaic humans. Some H. naledi crania, such as DH3, are substantially smaller than any H. erectus cranium, and the small size and thin vault bone of even the largest H. naledi skull, LES1, are outliers compared to H. erectus, matched only by some Dmanisi crania. The facial morphology of H. naledi is more distinct from those of H. erectus and H. habilis. The nasal bones of LES1 do not project markedly anteriorly, although like many specimens of H. erectus, LES1 has a projecting nasal spine. LES1 has a relatively flat lower face, with a transversely concave clivus and incisors that project only slightly past the canines. This morphology is similar but less extreme than that found in KNM-ER 1470 of H. rudolfensis, and is not shared with the other species pictured here. H. naledi has several distinctive features of the temporal bone that are absent from or found in only a few specimens of the other species pictured, including a laterally inflated mastoid process (comparable to some specimens of Au. afarensis), a weak or absent crista petrosa (comparable to Au. afarensis), and a small external auditory meatus (comparable to KNM-WT 40000 of Kenyanthropus platyops [Leakey et al., 2001]). In this illustration, KNM-ER 1813, KNM-ER 1470, KNM-ER 3733, and ZKD L2 are represented by casts. Because these images are in a nonstandard orientation, scale is approximate.

The maxilla and mandible of LES1 are also consistent with the Dinaledi H. naledi sample (Supplementary file 1; Figures 8, 9, 10 and 11). The maxilla has a mediolaterally flattened subnasal region, a parabolic dental arcade, and an anteriorly shallow palate. The mandible of LES1 has a gracile mandibular corpus, a vertical mandibular symphysis with weak mentum osseum, a steeply inclined lingual alveolar plane, weak inferior and absent superior transverse tori, continuous and deeply excavated anterior and posterior subalveolar fossae, mental foramina positioned above mid-corpus height, well defined ectoangular and endoangular tuberosities, and a root of the ascending ramus that originates at the mesial border of the M2. Again, many of these traits can be found individually in other hominin species, but in combination, they are uniquely found in H. naledi.

Mandibular and dental anatomy in H. naledi compared to other species of Homo.

Right demi-mandibles attributed to H. rudolfensis, H. habilis, H. naledi, H. erectus, and H. sapiens are pictured. All mandibles are aligned using the line marking the distal edge of the first molar. Each of the six horizontal lines corresponds to the edges of teeth in the DH1 mandible, the holotype specimen of H. naledi, with corresponding teeth labeled to the left. Using these lines, it is apparent which specimens have longer premolars and first molars, and which have longer second and third molars compared to DH1. The dentition of the LES1 mandible has been affected by interproximal wear, resulting in shorter mesiodistal measurements. Mandibular morphology and dental proportions vary slightly among most species of Homo, particularly in comparison with the large differences in dental proportions among species of Australopithecus and Paranthropus. Still, H. naledi is clearly distinguishable from other species of Homo (Berger et al., 2015; Laird et al., 2017). Fossils of H. rudolfensis, H. habilis, and H. erectus differ from H. naledi in the proportions of different parts of the postcanine tooth row and in features of the mandibular corpus. H. erectus. While fossils attributed to H. erectus vary in dental proportions, the early African and Georgian fossil specimens (here represented by KNM-ER 992, D211 and D2600) have larger first molars than H. naledi, comparable premolar sizes, and highly variable second and third molar sizes. The mandibles attributed to H. erectus mostly have greater corpus height than H. naledi mandibles and are highly diverse in corpus breadth, symphyseal thickness, and robusticity. Many have a strong post-incisive planum, most obvious in D2600 (shown). All three also differ from H. naledi in the crown complexity of their molars and premolar morphology, as illustrated in more detail in Figure 12. Some specialists would attribute these three mandibles of H. erectus to three different species. H. habilis. The two Olduvai mandibles of H. habilis are themselves quite different from each other in size. Both have similar dental proportions to H. naledi with bigger teeth across the postcanine dentition. Tobias (1967) viewed O.H. 13 as being similar to H. erectus and described it as an ‘evolved H. habilis’. Its occlusal morphology and dental proportions do resemble KNM-ER 992 (Wood, 1991), although the mandibular corpus is thinner and shallower, with a curved base in lateral profile. A strong post-incisive planum is evident in both mandibles. H. rudolfensis. The KNM-ER 1802 and Uraha (UR 501) mandibles have often been attributed to H. rudolfensis, although both attributions may be doubtful (Leakey et al., 2012). However, both lack any special similarities with contemporary australopiths and represent a megadont early Homo morphology with corpus size and robusticity much greater than those of H. naledi. Au. sediba. Molar sizes in the MH2 mandible are around 1 mm larger than the average for H. naledi, but the proportions are very similar to those of H. naledi, and like H. naledi, MH2 has a weak post-incisive planum and a small symphysis area. H. sapiens. The modern human mandible shown here, from a recent South African individual, has similar first molar size to the H. naledi mandibles, but much smaller premolars and second and third molars. The crown complexity in this individual, which is not unusual for African population samples, is substantially greater than evidenced in H. naledi. The mandibular corpus is smaller and much less robust than H. naledi. KNM-ER 1802, UR 501, O.H. 13, O.H. 7, and KNM-ER 992 are illustrated here with casts; the remainder are original specimens. The left side of O.H. 7 is shown here mirrored.

Comparison of H. naledi mandibles to other hominin species, from lateral view.

The DH1 holotype mandible and the LES1 mandible of H. naledi have a moderately deep mandibular corpus compared to other species of Homo; the LES1 mandible has a slightly greater corpus height anteriorly (at P3) than posteriorly (at M2). LES1 has rather a high coronoid process; the height of the condyle was probably lower than this. The mental foramen is at the midpoint or slightly higher in both H. naledi mandibles, and in both, the symphysis is nearly vertical. These features vary substantially within Homo. Modern humans (bottom) typically have a chin, but otherwise vary substantially in corpus height, whether the base of the corpus is parallel with the alveolar portion or with the occlusal surfaces of the teeth. Here that variability is illustrated with two modern human mandibles of male individuals, one from island Melanesia (left), and one from southern Africa (right). H. erectus exhibits very extensive variation in corpus height and thickness. D2600 (shown) is extremely thick and robust, but is not an outlier; other H. erectus mandibles approach or equal its corpus dimensions. The position of the mental foramen also varies, as does the relative anterior versus posterior corpus height and the symphyseal profile, from more sloping to near vertical (as illustrated by KNM-ER 992, although this specimen is damaged at the symphysis). MH2 (Au. sediba) has comparable corpus height and robusticity to the H. naledi mandibles, with a more sloping symphysis. O.H. 13 is a more gracile mandible than the H. naledi specimens in many respects. It has a curved base and a sloping symphysis. The more complete left side of LES1 is shown here and mirrored for comparison to other specimens. KNM-ER 992 and O.H. 13 are represented here by casts.

The teeth exhibit moderate occlusal wear on the second and third molars, trending toward near-complete dentine exposure on the occlusal surfaces of first molars and substantial removal of occlusal detail of the anterior dentition. The dental morphology of LES1 is entirely consistent with the Dinaledi sample of H. naledi (Figures 10 and 12). The mesiodistal and buccolingual (or labiolingual) crown dimensions of all the LES1 teeth fall within the range of the Dinaledi dental sample, except for those teeth where interproximal wear has clearly reduced the mesiodistal dimension (Table 2; Figure 13). The P3 crowns are worn, but they are roughly symmetrical about their mesiodistal axis in occlusal view; they are fully bicuspid and multirooted, with a smaller circular mesiobuccal root and larger, more platelike, distal root. This configuration is repeated throughout the Dinaledi dental assemblage. The shared overall P3 morphology of LES1 and the Dinaledi sample is distinctive in H. naledi and not observed in other species of hominins (Figure 12; Berger et al., 2015). The P3 and P4 are both three-rooted, with two ovoid roots present buccally and a larger ovoid root present lingually. The roots are not widely splayed as in some other multi-rooted hominins, and especially for the P4, the buccal roots are closely packed in buccal view. This root configuration is seen in the H. naledi type specimen, U.W. 101–1277. The mandibular canine crowns have asymmetrically placed crown shoulders, with the mesial more apically placed than the distal. Further, the distal shoulder is formed by an accessory cuspule. These features are strongly distinctive in H. naledi (Berger et al., 2015), with only a few specimens of H. erectus approaching this canine configuration. None of the molars exhibit any evidence of supernumerary cusps, and cingular features, such as the protostylid and Carabelli’s feature, are either absent or weakly developed and are expressed independently of the grooves of the crown. The molar size gradient in the LES1 mandible is M1 < M2 < M3 as in the Dinaledi Chamber sample of H. naledi (Figure 10). The Dinaledi Chamber includes no maxillary dentition with all three molars in place, but U.W. 101–1269 is a LM3 that exhibits a mesial interproximal facet that matches the distal facet of the LM2 present in the U.W. 101–1277 (DH1) maxilla. If these specimens do represent a single individual, then the maxillary molar gradient for this specimen would be M1 < M3 < M2, which is also seen in the LES1 maxilla. In total, these dental features are within the known range for H. naledi in every instance and distinguish LES1 clearly from all other hominin species.

Occlusal view of H. naledi mandibular teeth compared to those of other hominins.

Teeth from the canine to the third molar are shown, if present, in the orientation in which they are found within the mandible. All individuals are aligned vertically by the distal margin of the first molar. Mandibles from the Lesedi Chamber, U.W. 102 c-589 and LES1 are shown next to DH1 and U.W. 101–377 (Berger et al., 2015). The mandibles illustrated from H. erectus have relatively little occlusal wear, so their morphology can be seen more clearly than that of worn mandibles. The immature U.W. 101–377 (H. naledi) is comparable in developmental age and wear to O.H. 7 (H. habilis), as well as to D2735 and KNM-WT 15000 (H. erectus). When compared to H. habilis, H. erectus, and australopiths, H. naledi is notable for its relatively small first molars, its relatively small canines, and its lack of supernumerary cusps and crenulation on the molars. The complexity of molar cusp and groove patterns is especially evident in the chronologically early H. erectus specimens from Africa and Georgia shown here. For example, the unworn M2 of the immature U.W. 101–377 mandible of H. naledi has a relatively simple crown anatomy with very little wrinkling or crenulation. By comparison, the M2 of D2735, D211, and KNM-WT 15000, all with minimal occlusal wear, show extensive crenulation and supernumerary cusps. Canine size and molar crown complexity vary substantially among modern human populations, but the southern African individual illustrated on the right is not atypical for its population, and has greater molar crown complexity and larger canine dimensions than any of the H. naledi mandibular dentitions. The morphology of the third premolar varies extensively among these hominin species and within H. erectus. The H. naledi P3 anatomy can be seen clearly in the immature U.W. 101–377 individual. It is characterized by roughly equally prominent lingual and buccal cusps and an expanded talonid. In H. naledi, this tooth is broadly similar in morphology and size to the P4. This configuration of the P3 is not present in the other species, with only KNM-WT 15000 exhibiting some expansion of the lingual cusp in what remains an asymmetrical and rounded P3. A.L. 400–1, O.H. 7 and KNM-WT 15000 are represented by casts; The left dentition of U.W. 102 c-589 and O.H. 7 have been mirrored to compare to right mandibles. Images have been scaled by measured first molar dimensions.

Metric comparisons of the Lesedi Chamber dental material.

H. naledi is clearly differentiated in first molar and canine dimensions from other species with broadly similar cranial and dental morphology, including Au. sediba, H. habilis, H. rudolfensis, and early H. erectus samples from Africa and Georgia. The material from the Lesedi Chamber is within the range of or similar to H. naledi in these dimensions and well differentiated from the other samples. Top left: mandibular first molar dimensions. Top right: maxillary first molar dimensions. Bottom left: mandibular canine dimensions. Bottom right: maxillary canine dimensions. The LES1 first molars and maxillary canines have a substantial degree of interproximal wear, and the values plotted here are not corrected for this wear, which shortened the mesiodistal dimension by as much as a millimeter. The values plotted here should thus be regarded as minimum values. The H. erectus sample here includes specimens from the Lake Turkana area, Konso, Tighenif (Ternifine), Thomas Quarry, and Dmanisi; Asian H. erectus specimens are omitted. Attributions of H. habilis and H. rudolfensis specimens are indicated in the Materials and methods.

*Denotes measurements where the tooth is extremely worn, and mesiodistal diameter reported here has not been corrected for the degree of wear.

†Denotes instances where we report a minimum value for labiolingual measurements because the crown is not complete or is broken.

The LES1 cranium does exhibit some traits that differ from comparable examples in the Dinaledi Chamber. The cranium is slightly larger overall, with an estimated endocranial volume of approximately 610 ml, and this larger size is reflected in the external vault measurements. Previously, the largest known H. naledi endocranium was DH1 at approximately 560 ml (Berger et al., 2015). LES1 contrasts in morphological features with the small DH3 cranium in ways that have been observed when comparing male individuals with female individuals in other hominin species. The supraorbital torus of LES1 is more pronounced than that in the small DH3 individual. LES1 has a stronger supramastoid/suprameatal crest, a larger mastoid process, and a more marked pterygoid insertion when compared to the U.W. 101–361 mandible. Although LES1 is outside of the endocranial volume range of specimens presently attributed to H. naledi, the larger size and more robust features of LES1 are consistent with the combination of cranial and mandibular characters in H. naledi.

Comparative cranial anatomy

The comparative anatomy of the H. naledi cranial remains from the Dinaledi Chamber was presented in detail by Laird et al. (2017), and morphometric comparative analyses of that collection and of other hominin samples were presented by Schroeder et al., 2017. Additionally, Rightmire et al., 2017 addressed the morphological features of H. naledi in comparison with the Dmanisi fossil crania, in particular the robust D4500 cranium. The anatomy of the LES1 cranium reinforces the conclusions of those studies in most respects (Supplementary file 1, 2; Figure 7).

Crania of H. naledi are most similar in cranial vault shape to other Homo or Homo-like australopith crania with small endocranial volume, including D2700, D2280, MH1, KNM-ER 1470, and KNM-ER 1813 (Schroeder et al., 2017). These shape similarities do not reflect small size alone: for example, H. naledi cranial material is quite distinct in shape from LB1, and the small DH3 calvaria of H. naledi is also notably different from KNM-ER 42700 in shape analyses (Schroeder et al., 2017). Additional differences between H. naledi and other small specimens of Homo are evident among the morphological characters of the skull (Laird et al., 2017). Compared to specimens attributed to H. erectus, H. habilis or H. rudolfensis, the temporal bone of H. naledi exhibits a small external auditory meatus, a shallow and relatively narrow mandibular fossa, a small postglenoid process, and a laterally inflated mastoid process. The features of the occiput that distinguish H. naledi from H. erectus (Laird et al., 2017) are not part of the preserved sections of LES1. However, the maxilla of LES1 is better preserved than DH1, and like the latter specimen, presents a transversely flat nasoalveolar clivus, similar to H. rudolfensis but not H. erectus or H. habilis, a shallow anterior palate, unlike H. erectus or H. habilis, and an anteriorly projecting anterior nasal spine, comparable to H. erectus but not present in H. habilis or H. rudolfensis. The LES1 cranium is similar to the Dinaledi H. naledi sample in its morphological differences from the H. floresiensis LB1 cranium (Berger et al., 2015). All H. naledi crania are estimated to have been larger than LB1 in endocranial volume, while LES1 and the other H. naledi cranial remains lack the reduced cranial height, marked frontal keel, canine juga and anterior pillars of the LB1 cranium. The cranial anatomiesof H. naledi and LES1 share a unique set of traits that otherwise distinguish Homo species from each other.

The LES1 mandible shares very similar overall dimensions, shape, and morphological features with DH1 from the Dinaledi Chamber (Supplementary file 1; Figures 8, 10 and 11). Comparative analysis of overall mandibular shape places H. naledi closer to australopith mandibles such as Sts 36 and Sts 52b than to any specimens of H. habilis, H. rudolfensis, or H. erectus, despite the large range of shape variation among H. erectus mandibular specimens (Schroeder et al., 2017). Dmanisi mandibular specimens, including D2735 and D2600, are different from the DH1 mandible despite the similarity in vault shape between D2700 and D2280 and H. naledi DH3, and these mandibular differences are likewise reflected in the LES1 mandible. The morphological features of the LES1 mandible align it clearly with DH1 and other partial H. naledi mandibles from the Dinaledi Chamber, setting it apart from other species of Homo, including those with similar-sized molars (Figures 10 and 12). Unlike the H. floresiensis mandibles LB1 and LB2, the mandibular symphyses of LES1 and DH1 have steeply inclined posterior faces that lack any post-incisive planum or superior transverse torus. The mandibular molar gradient of H. naledi and the morphology of the mandibular premolars also distinguish it from H. floresiensis (Brown and Maeda, 2009; Kaifu et al., 2011, 2015). The symphyseal morphology of H. naledi likewise distinguishes LES1 and DH1 from mandibular remains attributed to H. habilis and H. rudolfensis, such as OH 7, OH 13, KNM-ER 60000 and KNM-ER 1802.

Claviculae

U.W. 102a-021 is a nearly complete right clavicle, missing only the articular surface of the sternal end, where trabecular bone is exposed over the entire articular area, including a small bit of the anterior surface (Figure 14). The shaft is broken into two pieces near the midshaft but the two pieces conjoin cleanly. There is also a small bit of damage to the acromial end. On the posterior surface, the medial part of the crest for the conoid tubercle is broken off. The specimen exhibits a dark surface coating on the anterior aspect of the sternal half and patchy areas of black staining on its acromial half. There are fine hairline longitudinal cracks on much of the acromial half of the bone.

U.W. 102a-021 right clavicle from the Lesedi Chamber.

U.W. 102a-206 is a ca. 41-mm-long fragment of left clavicular shaft, preserving the midshaft region (based on anatomical comparisons with U.W. 102a-021). The shaft anteroposterior (AP) and superoinferior (SI) dimensions are slightly smaller than those of the right side clavicle at this position. The fragment compares favorably to U.W. 102a-021 in overall size, curvature, and shaft morphology. U.W. 102a-239 is the acromial end of a left clavicle, including the lateral 51.5 mm, preserving the conoid tubercle (but not its medial crest) and the articular surface for the acromion of the scapula. This is slightly larger than the acromial end of U.W. 102a-021, but otherwise fairly similar in morphology.

Comparative clavicular anatomy

The clavicular anatomy of H. naledi is comparable to that present in Au. sediba (Churchill et al., 2013) and H. habilis (Oxnard, 1969; Ohman, 1986; Voisin, 2001), suggesting a superiorly positioned shoulder (Feuerriegel et al., 2017). The U.W. 102a-021 and U.W. 102a-206 claviculae are consistent with the morphology noted in the clavicular material from the Dinaledi Chamber. As with clavicular specimens from U.W. 101, the overall appearance of the clavicle is smooth (non-rugose), with only a few weakly developed entheses. The deltoid crest is present as a mildly rugose line on the anterior surface of the lateral curvature. The conoid tubercle appears well-developed and forms a posteriorly projecting flange, producing a pronounced border to a deep subclavian sulcus. However, unlike some specimens from the Dinaledi Chamber (such as U.W. 101–258), the conoid is not centrally positioned on the shaft, but rather occurs on the posterior margin.

Humerus

U.W. 102a-002 is a proximal shaft fragment of a right humerus (Figure 15). The head and greater tubercle are missing, as is all but the very distal base of the lesser tubercle. From this metaphyseal region, the fragment preserves approximately 50–60% of the shaft, with a total fragment length of 85 mm. U.W. 102a-013 includes two fragments identified as humeral head, each with some articular subchondral bone, which may derive from the same element as U.W. 102a-002. They appear to be consistent in curvatures of the articular surface with U.W. 102a-257. The specimen is mostly coated with a brown to dark-brown mineral patina, the surface is unweathered with only slight surface removal on the distal end of the anterior surface. The breaks, both proximal and distal, are sharp.

U.W. 102a-002 right humerus fragment.

U.W. 102a-257 is a fragment of left humerus, including the head and proximal shaft, and is largely complete from head to just around midshaft (Figure 16). There is corrosion to the superior aspect of the proximal articular surface (which precludes an accurate measurement of the superoinferior diameter of the head), and to the articular margin of the superolateral head. The surface of the specimen is otherwise very well preserved with no signs of weathering. A dark-brown to black patina covers much of the posterior surface of the shaft, wrapping around to the anterior surface on the most distal part. The proximal 40 mm or so of the lateral crest of the deltoid tuberosity is present. U.W. 102a-257 is consistent with the morphology and size of U.W. 102a-002, and they may represent left and right humeri of the same individual.

U.W. 102a-257 left proximal humerus fragment.

The proximal humerus fragments from the Lesedi Chamber have morphology consistent with the Dinaledi Chamber collection of H. naledi, both in the size of the head and in the shaft diameter. In both assemblages, the bicipital groove appears deep and narrow, and the lesser tubercle is projecting. The most distinctive aspect of the humerus material of H. naledi in comparison with other hominin species is the very low humeral torsion angle in the adult U.W. 101–283 humerus, in which the head faces nearly directly posteriorly (Feuerriegel et al., 2017). This aspect cannot be assessed directly in the fragments from the Lesedi Chamber.

Ulna

U.W. 102a-015 is a right proximal ulna, on which much of the trochlear notch and olecranon process are preserved in addition to the proximal half of the diaphysis (Figure 17). There is erosion to the anterior tips and margins of the coronoid and olecranon process. The surface of the shaft is well-preserved and exhibits very slight hairline longitudinal cracks. The break to the distal end is sharp and cleanly transverse. The olecranon process is mediolaterally narrow and the trochlear notch appears to have opened anterosuperiorly, as in modern humans but not Neandertals. While there is only one fragmentary (and probably immature) proximal ulna from the Dinaledi Chamber, U.W. 102a-015 generally compares well with U.W. 101–560 in terms of morphology and gracility.

U.W. 102a-015 ulna fragment.

Hand and wrist

Four adult hand and wrist elements have been recovered from the 102a locality (Figure 18). U.W. 102a-028 is a right fourth metacarpal (RMc4), with a small base and a relatively radioulnarly broad head (Figure 15). The metacarpal shaft shows substantial curvature and is relatively robust for its length, although it still falls within the upper range of variation found in modern humans (Figure 16). U.W. 102a-117 is a complete right scaphoid; U.W. 102a-476 is a complete right capitate; and U.W. 102a-477 is a partial right lunate. The scaphoid, lunate, and capitate are consistent in size and appear to match each other when placed in anatomical articulation; the RMc4 is likewise a good match in size, with a lateral base matching in dorsopalmar contour the base of the capitate. Thus, these four bones may represent the right hand of one individual.

U.W. 102a-028 right fourth metacarpal.

These four bones are qualitatively similar in overall shape to that described for H. naledi, but they are absolutely larger in most of their overall dimensions (Kivell et al., 2015). The lunate is missing a large portion of its articular surface for the radius and adjacent areas, precluding quantitative comparisons of its morphology. A canonical variates analysis of scaphoid and capitate comparative morphology in African apes and hominins demonstrates that the Dinaledi and Lesedi scaphoids and capitates fall together within a distinct space relative to other fossil and extant hominids. Along the first canonical axis, Dinaledi and Lesedi wrist remains cluster with modern humans and Neandertals because they all share derived features relative to those of African apes (Figure 19; Supplementary file 3). For instance, the scaphoid’s trapezium facet extends further onto the tubercle, and together, the trapezium and trapezoid facets are relatively large, as in modern humans and Neandertals (Supplementary file 3). The Dinaledi and Lesedi scaphoid and capitate morphology are distinguished from those of modern humans and Neandertals on the second canonical axis because the Mc2 facet orientation in H. naledi is roughly intermediate between that of modern humans and Neandertals on the one hand and that of African apes on the other. In this respect, the H. naledi capitates are more similar to those of H. floresiensis and several australopiths.

Quantitative comparisons of hand and wrist material from the Lesedi Chamber.

Left: ratios of fourth metacarpal dimensions in H. naledi compared to those in other hominin and great ape samples. Right: canonical variates analysis of capitate and scaphoid morphology in humans, chimpanzees, gorillas, and fossil hominins. H. naledi from the Dinaledi Chamber occupies a unique position in scaphoid and capitate joint configurations, which is closely matched by the capitate and scaphoid from the Lesedi Chamber. In this analysis, no a priori groups are assumed; we also examined the scenario in which Homo naledi and other fossil specimens are included as a priori groups and the results are essentially identical.

Vertebrae

Seven vertebrae have been recovered in the 102a assemblage, all from the lower thoracic and lumbar region of the spine. These vertebrae are roughly equivalent in preservation. The thin cortical bone of the vertebral bodies is eroded in large patches on these elements with exposure of underlying trabeculae. They have minimal surface staining or patination, and where the vertebral arches are present, the cortical surface is well-preserved.

U.W. 102a-036 is a largely complete antepenultimate thoracic vertebra, inferred as T10, with limited erosion to the anterior surface of the vertebral body and some damage distally on the transverse processes, particularly on the right side, and to the posterior end of the spinous process (Figure 20). The vertebral body is ovoid to kidney-shaped and the ring apophyses are relatively thick, covering approximately three-quarters of the vertebral body surface. The spinal canal is ovoid in shape and about one-third the size of the vertebral body. Facets for the tenth rib are posteriorly positioned, almost entirely on the pedicles. The pedicles themselves are transversely thick, as are the transverse processes, which are strongly posteriorly oriented. Together, the transverse processes and pedicles form nearly continuous, robust lateral structures for anchoring epaxial muscles and for transmitting forces to and from the vertebral body, respectively.

U.W. 102a-036 vertebra, T10.

U.W. 102a-151 is a nearly complete penultimate thoracic vertebra, inferred as T11, with some erosion and loss to the left side of the vertebral body and missing the left-side transverse process (Figure 21). Portions of the superior vertebral body surface are eroded away, revealing trabeculae. The superior articular facets are planiform and posteriorly oriented. The inferior articular facets are asymmetrical – the right side is curved and anterolaterally oriented, whereas the left side is planiform and oriented anteriorly on the coronal plane, as in the transitional vertebra. Costal facets are large, extending from the posterior aspect of the body inferiorly and posteriorly onto the pedicle. The vertebral body is kidney- to heart-shaped and the spinal canal is ovoid, with a slightly triangular shape. The spinous process is relatively long and relatively horizontal in its orientation, with its major axis deflecting inferiorly at an angle of approximately 20° from the surface of the superior vertebral body.

U.W. 102a-151 vertebra, T11.

U.W. 102a-154a is a nearly complete last thoracic vertebra, inferred as T12. The right inferior articular facet, distal spinous process, and anterior aspect of the inferior vertebral body are broken away. The anterior portion of the body is eroded on the right side, as are the lateral aspects of the superior vertebral body. The superior articular facets are asymmetrical, matching the inferior articular facets of the superjacent vertebra (U.W. 102a-151): the left superior articular facet is planiform and posteriorly oriented on the coronal plane, whereas the right superior articular facet is curved and posterolaterally oriented. The right superior articular facet is comparatively diminutive in size, particularly in transverse dimension. The vertebral body is kidney- to heart-shaped and transversely wide. The costal facets are positioned at the body-pedicle border but are eroded on both sides; thus, their morphology cannot be fully appreciated. The pedicles themselves are anteroposteriorly short and contribute to a wide, ovoid spinal canal.

U.W. 102a-154b, U.W. 102a-322, and U.W. 102a-306 are vertebral bodies associated with little or no vertebral arch structures. U.W. 102a-139 is a lumbar vertebra preserving most aspects of the vertebral body and neural arch, but it is broken into five pieces that refit reasonably well, although the spinous process is missing. None of the bodies or preserved aspects of pedicles bear costal facets. U.W. 102a-154b nicely articulates with U.W. 102a-154a superiorly and U.W. 102a-322 inferiorly, and U.W. 102a-306 and U.W. 102a-139 articulate with each other; however, U.W. 102a-322 and U.W. 102a-306 do not articulate. The lumbar transverse processes of U.W. 102a-139 are anteroposteriorly wide, emerging anteriorly from the posterior aspect of the vertebral body along the pedicles and posteriorly to the bases of the superior articular processes. Its body is clearly posteriorly wedged in lateral view. Together, these features indicate that U.W. 102a-139 is the last lumbar vertebra. Therefore, the likely seriation is as follows: U.W. 102a-154b is L1, U.W. 102a-322 is L2, U.W. 102a-306 is L4, U.W. 102a-139 is L5, and L3 is missing.

Comparative vertebral anatomy

The U.W. 102a-036 T10 and U.W. 102a-151 T11 vertebrae are directly comparable to the near-complete U.W. 101–855 T10 and U.W. 101–1733 T11 vertebrae from the Dinaledi Chamber. The Dinaledi and Lesedi Chamber pairs are comparable in size, but the Lesedi vertebrae clearly belong to a larger, more robust (presumed male) individual. Although the Dinaledi transverse processes are broken at their bases, the preserved aspects are strongly posteriorly oriented, albeit to a lesser degree than those from the Lesedi Chamber (Figure 22). The lower thoracic transverse processes of Au. afarensis, Au. africanus, and Au. sediba possess more laterally oriented transverse processes. Only SKX-41692, a presumed P. robustus T10, possesses similarly posteriorly oriented transverse processes among australopiths. However, its relatively large vertebral body, small spinal canal, and overall shape contrast with the lower thoracic transverse processes of H. naledi (Williams et al., 2017). The combination of a relatively large vertebral body and spinal canal is present in both the Dinaledi and the Lesedi Chamber T10 vertebrae, but not inAustralopithecus and Paranthropus specimens. The Dinaledi T11 bears planiform articular facets superiorly and inferiorly and is therefore not the transitional vertebra. In the Lesedi Chamber vertebral column, the change in articular facet orientation occurs asymmetrically across the T11 and T12 vertebrae, as occurs in <4% of modern humans (Williams et al., 2017). In all known Australopithecus and H. erectus specimens, the transitional vertebra is T11 (Haeusler et al., 2002, 2011; Williams et al., 2013; Meyer et al., 2015).

Vertebral transverse process orientation.

H. naledi is distinctive when compared to many other hominin species in having T10 and T11 vertebral transverse processes oriented with a relatively low angle. Left: U.W. 102a-036 compared to U.W. 101–855 from the Dinaledi Chamber (top), and U.W. 102a-151 compared to U.W. 101–1733 (bottom). All of these vertebrae have transverse processes oriented more posteriorly than those of most other hominins, U.W. 102a-036 is the most extreme. Right: charts showing the comparative orientation of transverse processes in humans, living great apes, and fossil hominins. For the T10 (top), the U.W. 102a-036 value (labeled ‘Lesedi’) is lower than that for any other hominins, while the Dinaledi T10 is similar to the Neandertal value and extremely low compared to that for modern humans. The T11 (bottom) shows a similar but less extreme pattern.

Costae

U.W. 102a-250 is a nearly complete right first rib, with erosion and breakage to the head, tubercle, lateral border and distal end. The neck is flattened in its superior-inferior dimension and descends in the vertebro-inferior direction. The tubercle and the posterior angle coincide. The facet of the articular tubercle was damaged post-mortem.

Two partial first ribs (U.W. 101–083 and U.W. 101–621) of H. naledi are preserved in the Dinaledi Chamber hominin sample, but neither rib has its head nor enough of the shaft preserved to allow accurate estimation of curvature (Williams et al., 2017). The angulation and shape of these fragments appears comparable to those of MH2 Au. sediba and A.L. 288–1 Au. afarensis. U.W. 102a-250 is more complete than the Dinaledi first rib fragments, and is similar in morphology in the overlapping regions. This rib is slightly more curved than the Sterkfontein first rib, StW 670 (Tawan et al., 2016). The anatomy of U.W. 102a-250 is entirely compatible with attribution to H. naledi, although the bone is also similar in morphology and size to known australopith first ribs.

Thirteen additional specimens from 102a are partial ribs or rib fragments, none are identifiable to element and none present anatomical information that is useful for testing the taxonomic affiliation of the sample.

Ossa coxae

U.W. 102a-138 (Figure 23) is a fragmentary right ilium of an immature individual (as evident by the presence of triradiate cartilage, by an unfused apophysis at the anterior inferior iliac spine, and by very small overall size). The fragment is very light, with thin cortical bone, and is eroded around margins of the acetabular portion. The iliac blade is mostly missing, but the auricular surface, greater sciatic notch, acetabulosacral buttress, and anterior margin of the iliac blade are present. Despite the thin and fragile nature of this element, the surface is well-preserved.

U.W. 102a-138 immature right os coxa fragment.

The adult pelvic material of H. naledi from the Dinaledi Chamber is notable in combining an Au. afarensis-like degree of iliac flare, a weak and anteriorly placed iliac pillar, and a narrow tuberoacetabular sulcus on the ischium (Berger et al., 2015; VanSickle et al., personal communication). U.W. 102a-138 represents the most complete immature ilium fragment of H. naledi found to date, and its morphology is comparable to that of the juvenile U.W. 101–486 ilium fragment, and thus consistent with the morphology seen in H. naledi. It lacks the diagnostic characters that could differentiate it clearly from ilium fragments from other hominin species, as the iliac blade and iliac pillar are both poorly preserved. The lack of an accompanying ischial fragment precludes an evaluation of tuberoacetabular sulcus morphology in the 102a material.

Femora

U.W. 102a-001 is a proximal right femur, in which much of the head and neck, and the proximal subtrochanteric shaft are preserved (Figure 24). The head is badly eroded, especially anteriorly, and only a few small patches of subchondral articular bone are preserved on the posterior aspect. The posterior side of the neck is fairly well preserved from the head all the way to the lesser trochanter, which is planed off, with only the base remaining. The anterior side of the neck is missing. Trabecular bone is exposed from the anterior head all the way to the lateral surface at the base of the greater trochanter. The greater trochanter is missing entirely, save for a small bit of its distal lateral surface. The surface overall is marred by areas of post-depositional damage, including a number of transverse scratches on the shaft.

U.W. 102a-003 left proximal femur fragment.

U.W. 102a-004 is a fragment of left distal femur, preserved from roughly midshaft to the distal subchondral bone surface of the intercondylar notch (Figure 26). Both condyles are missing. The shaft has surficial markings similar to those present on U.W. 102a-001. This fragment is morphologically compatible with U.W. 102a-003 in shaft diameter and cross-section, and the two specimens exhibit no morphological overlap, suggesting that they may represent the same femur.

U.W. 102a-004 left distal femur fragment.

U.W. 102a-003 and U.W. 102a-004 may conjoin with each other. Both fragments are morphologically compatible in shaft diameter and cross-section, and at the broken distal end of U.W. 102a-003 and at the proximal end of U.W. 102a-004, a small part of the circumference of the shaft (approximately 10 mm in total) on the posterolateral side appears to provide a refit. However, the edges of this apparent break are abraded, reducing the certainty of the association. Joining the bones at this point, U.W. 102a-003 and U.W. 102a-004 preserve 321 mm of a femoral shaft. Using the similarly sized U.W. 101–002 to represent the missing proximal end and KNM-ER 1481 to represent the distal end (Figure 27), we preliminarily estimate the femoral length of this individual to be ~375 mm.

Length estimation of femur based on U.W. 102a-003 and U.W. 102a-004.

Two specimens were used to estimate the missing proximal and distal ends of the femur. Top: U.W. 101–215 is a distal femur fragment that presents a similar morphology to the U.W. 102a-004 distal femur, while preserving the distal articular surface. Middle: U.W. 102a-004 and U.W. 102a-003 conjoined, in posterior view. Bottom: U.W. 102a-001 is comparable in size with U.W. 102a-003, and while the morphology of the muscle markings is different, the alignment of the lesser trochanters gives a good basis for estimating the proximal extent of the bone. The length estimate is 375 mm.

U.W. 102a-001 (right proximal) and U.W. 102a-003 (left proximal) are similar in size. They preserve an overlapping area of anatomy from just above the lesser trochanter down to around the midshaft area. However, despite their similarity in size, the two contrast in several anatomical details. U.W. 102a-001 is more platymeric in the subtrochanteric area, with a greater mediolateral (ML) breadth than U.W. 102a-003. The lesser trochanter is abraded in both specimens, but the morphology of the inferior and medial aspects of it appear different in the two bones. U.W. 102a-001 has a shallow sloping border to the lesser trochanter medially, and the inferior aspect tails off into a broad, less marked line leading to a very slight linea aspera by midshaft. By contrast, U.W. 102a-003 has a steep medial aspect to the lesser trochanter, and it tails into a sharply defined crest that broadens around 15 mm down the shaft into a rugose, double crest, which narrows by midshaft into a strong linea aspera. The insertion for m. gluteus maximus is prominent and rugose in both femora but in U.W. 102a-001, the rugosity extends further down the shaft. Overall, the asymmetry of these two bones would be very unusual in the left and right femora of a single individual. We accept this provisionally as evidence for a second adult individual in the 102a assemblage.

Comparative femoral anatomy

The femoral morphology of H. naledi is a mosaic of features seen in Australopithecus species such as Au. afarensis, Au. africanus and Au. sediba, and features otherwise known in Homo, including Plio-Pleistocene H. erectus and fossils attributed to Homo sp. indet., such as KNM-ER 1472 and KNM-ER 1481 (Figure 28; Marchi et al., 2017). The femoral remains from the 102a locality share this mosaic of features, including: a marked linea aspera, with a weak pilaster in U.W. 102a-003; a strong muscle insertion for m. gluteus maximus; a platymeric shaft just inferior to the lesser trochanter; a long and anteroposteriorly flattened femoral neck; and an AP expanded femoral midshaft. The Dinaledi remains of H. naledi have markedly anteverted femoral necks. Damage to the femoral neck of the U.W. 102a-001 specimen limits the accuracy of an estimate of anteversion, but at 115 degrees, this estimate is within the range for the Dinaledi specimens. The most distinctive feature of the H. naledi proximal femur is the presence of two mediolaterally oriented pillars on the superior femur neck, separated by a medially positioned shallow and vascularized groove where m. obturator internus and gemelli insert (Marchi et al., 2017). This configuration is not seen in other hominin species. The U.W. 102a-001 femoral neck is damaged superiorly, precluding a clear assessment of whether two distinct pillars were present. What is preserved posteriorly demonstrates the presence of a medially positioned vascularized groove, but not of the inferior pillar present in the Dinaledi femora. With this exception, the U.W. 102a-001, U.W. 102a-003 and U.W. 102a-004 femoral fragments are entirely consistent with the morphology known for H. naledi, and the combination of features in the U.W. 102a-001 proximal femur is not consistent with known fossil examples attributed to other species of Homo or Australopithecus.

Comparison of H. naledi femora to those attributed to early Homo.

Top: roximal femora attributed to Au. afarensis, Homo sp., H. naledi, and H. erectus, all shown in posterior view. The femora have been aligned by matching the inferior point on the lesser trochanter to the horizontal line on the figure, and all are shown at approximately the same shaft angle. Many of the H. naledi femora have notably thin shafts, although the largest shown here, U.W. 101–1475, is greater in shaft thickness than the complete KNM-ER 1480, KNM-ER 1472, or D4167 femora. The specimens here attributed to ‘Homo sp.’ were surface finds without associated cranial material. Their anatomy has been considered consistent with Homo, although some have suggested that KNM-ER 738 may instead be Paranthropus. U.W. 102a-001 is a right femoral fragment, and left femora here have been mirrored for comparison, including KNM-ER 738, KNM-ER 1481, U.W. 101–398, U.W. 101–1475, KNM-WT 15000, and A.L. 288–1. Bottom: H. naledi femur length compared to those of other fossil femora. U.W. 102a-003 is shown conjoined with U.W. 102a-004. The top and bottom horizontal lines correspond to the proximal and distal limits of the maximum length estimate for this femur as illustrated in Figure 24. Femur maximum lengths and length estimates are as reported by McHenry (1991), D4167 length is from Lordkipanidze et al. (2007). As above, all femora are aligned by the lesser trochanter, which is preserved in all of these shaft fragments. The H. naledi U.W. 102a-003 femur has a shaft diameter comparable to that of A.L. 288–1, or even slightly shorter, but at an estimated 375 mm, it is nearly the same length as the D4167 femur of H. erectus at 387 mm. The U.W. 101–484 tibia specimen from the Dinaledi Chamber is also long and relatively narrow, and has an estimated length greater than that of the D3901 tibia from Dmanisi (Marchi et al., 2017). Several very thick, large femora have been attributed to H. erectus from the Early Pleistocene of Africa; these are very different from U.W. 102a-003 in their size, robustness, and more platymeric proximal shafts. U.W. 101–938 is an immature femur with no fusion of the head or distal epiphysis; it represents a younger developmental age than KNM-WT 15000, the immature H. erectus skeleton. Even at its young age, this H. naledi specimen is nonetheless longer than the A.L. 288–1 femur of Au. afarensis. A.L. 288–1 is shown here as reconstructed by P. Schmid. For comparison to the right U.W. 102a-003 femur, left femora are shown mirrored here, these include KNM-ER 1472, U.W. 101–938, and D4167. In this figure, KNM-ER 739, KNM-ER 1472, KNM-ER 1481, KNM-WT 15000, O.H. 28, and A.L. 288–1 are represented by casts.

Individuals represented in 102a

The hominin material from 102a appears to represent a minimum of two adult individuals and one immature individual. The inference of two adults is based upon the morphological incongruence of the left (U.W. 102a-003) and right (U.W. 102a-001) femoral elements (discussed above). Still, no adult element is clearly duplicated in the collection. The U.W. 102a-138 ilium, along with an immature sacrum fragment and two immature long bone fragments not described here, demonstrates the presence of at least one immature individual.

The lack of duplication of elements suggests that much (but not all) of the adult material may represent a single individual skeleton, which parsimoniously would also include the LES1 cranium. We accept this hypothesis provisionally. All elements in the current 102a collection were recovered from within an excavation area less than 50 cm x 70 cm, and 40 cm deep. Two vertebrae (U.W. 102a-154a and U.W. 102a-154b) were in articulation in situ. The articular morphology and sizes of seven vertebrae suggest strongly that they represent a single individual; the remainder of these elements were recovered in close physical proximity but not in articulation. All fragments attributed to the LES1 cranium were likewise recovered from a small area. The hand and wrist material is consistent with a single right hand on the basis of articular morphology. None of the other elements lend themselves to an evaluation of articular compatibility, but they are consistent in size. We consider it unlikely that the number of elements in the current collection would be recovered from a commingled assemblage consisting of substantial parts of multiple skeletons without also introducing duplicate elements.

This raises the problem of what seems to be a mismatch of the U.W. 102a-001 and U.W. 102a-003 femora. These two are similar in size, and the difference in their shaft dimensions is not greater than that found in 95% of a large sample of paired left and right human femora. However, they are different in muscle attachments and diaphyseal morphology, to the extent that would represent unusual asymmetry in a single individual. The data do not allow us to discard the hypothesis that one of the femora represents a second adult individual in 102a, albeit an individual of similar body size. The descriptive and measurement data do not indicate which (if either) of these femora may belong to the individual represented by LES1, nor which (if any) of the other postcranial elements are associated with either femur. On the basis of the non-duplication of elements, it seems likely that if there is a second individual, this second individual is represented by only a small number of elements, possibly just the femur. The two humerus specimens, U.W. 102a-002 and U.W. 102a-257, differ slightly in shaft diameter where it can be compared, but no other morphological differences are apparent on the preserved fragments, and a slight degree of upper limb asymmetry is not unusual in humans or in fossil Homo. We conclude that most of the 102a adult material probably represents a single skeleton, but we cannot assume that the ratios of either femur with other elements in the sample would reflect the proportions of a single individual. To be conservative, any consideration of proportions should allow for the possibility that multiple individuals are present.

Hominin material from 102b

The material from area 102b includes 12 specimens identified as hominin. Most of this collection consists of small fragments of cranium, many of which are identifiable to element, but which preserve no diagnostic morphology that would assist in taxonomic assessment. One partial mandible and five possibly associated teeth preserve morphological characters that are useful for taxonomic attribution.

U.W. 102b-438 is a fragment of right mandibular corpus from an immature individual (Figure 29). The alveoli for the RM1 are present; the alveoli for the rdm2 are also present and reveal the crypt with RP4 crown intact within. The fragment is broken anteriorly at the crypt for RP3 and posteriorly at the crypt for RM2, neither permanent tooth is present. The preserved corpus height at the midpoint of rdm2 is 14.9 mm; this is perhaps 1–2 mm less than the true value because of the erosion of the alveolar bone surface. Corpus breadth at the anterior edge of M1 is 15.2 mm; total length of the fragment as preserved is 43.5 mm.

U.W. 102b-438 immature mandibular fragment.

Several teeth excavated from 102b are compatible with the same approximate developmental stage as the U.W. 102b-438 mandibular fragment, and were recovered in close proximity to each other and to the mandible; no elements are duplicated. We hypothesize that these fragments represent the same individual, at least until the recovery of additional material makes us reassess this possible association. U.W. 102b-437 is the complete crown and two nearly complete roots of a ldm2 with moderate occlusal wear, including dentine exposure at the centra of cusps, and roots that appear to have begun to resorb at the tips. U.W. 102b-503 is a RP4 crown, nearly complete but not erupted. U.W. 102b-511 is a LC1 crown, nearly complete with no occlusal wear. U.W. 102b-515 is a LI2 that is nearly crown complete and unerupted. U.W. 102b-178 is a broken but apparently unworn probable RI2 crown that was recovered separately from these other teeth, which may also represent this individual.

The teeth all fall within the size range of equivalent elements from the Dinaledi Chamber sample. The U.W. 102b-438 RP4 crown is partially obscured within its crypt and not complete, to the minimal extent it is visible at this time, it is consistent with H. naledi mandibular P4 morphology. The U.W. 102b-503 maxillary P4 is likewise consistent with comparable Dinaledi examples, although this tooth differs little among several species of Homo, including modern humans. Like the incisors of LES1, U.W. 102b-515 lacks prominent cervico-incisal crown curvature, has no prominent crests on its lingual surface, and is not shoveled.

The U.W. 102b-437 ldm2 is buccolingually narrow and mesiodistally long, with an ovo-rectangular shape. Five well-developed cusps are present in a Y-fissure pattern, and the talonid is wider than the trigonid. Compared to the two lower dm2 specimens from the Dinaledi chamber, the metaconid and protoconid are relatively small, although it is not clear whether or not this is an artifact of mesial wear. Although the mesial aspect is worn, it is clear that the mesial marginal ridge was thick; it forms the distal border of a fissure-like anterior fovea. A thick distal marginal ridge is also present and it borders a fissure-like posterior fovea. Both the mesio- and disto-buccal grooves are deep and are associated with a wide V-shaped furrow. No protostylid is present. The mesial and distal roots each have a buccal and lingual canal connected by a dentin plate. The crown morphology is nearly identical to that of the two analogous teeth from the Dinaledi chamber (U.W. 101–655 and U.W. 101–1686), and supports their taxonomic designation to H. naledi. Although few have been found, the lower dm2s of H. erectus s.l. are relatively longer and more rectangular than those of H. naledi. In addition, the substantially wider talonid compared to the trigonid of both the 102 tooth and the H. naledi lower dm2s differentiates these dm2s from those of most other Homo.

The most important of the 102b teeth for morphological assessment is the LC1. The U.W. 102b-511 crown preserves its occlusal morphology and replicates with better detail the same morphology observed in the LES1 mandibular canines (Figure 30). It has asymmetrically placed crown shoulders, with the mesial shoulder more apically placed than the distal. Further, the distal shoulder is formed by an accessory cuspule and the mesial crest is shorter and more convex than the vertically disposed distal crest. These features are identical to those found in the Dinaledi permanent mandibular canines and are among the defining features of H. naledi. The asymmetrical shoulders of the canine crown and distal accessory cuspule are found to some degree in a number of specimens attributed to H. erectus, H. rudolfensis, H. habilis and Australopithecus, but the small canine and incisor sizes are inconsistent with attribution to any of these other taxa. On the basis of these observations, the immature dentition from 102b is identifiable as H. naledi.

All of the cranial fragments recovered from 102b are compatible with an immature developmental stage, and may come from the same individual as U.W. 102b-438. The minimum number of individuals (MNI) in 102b is therefore one individual at present. Without more information about the depositional history of the 102b locality in comparison with that of 102a, we cannot say for sure whether any of the specimens collected at this locality may represent the same immature individual that is represented by the pelvic fragments in 102a. The evidence does not currently exclude the hypothesis that the U.W. 102a-138 ilium and other immature pelvic fragments may represent the same individual as the U.W. 102b-438 mandible. The 102a and 102b areas are separated by approximately 3 m, and there is a possibility that slumping of material might have brought the remains of a single individual into both areas. Further work to establish the life-history stage of the immature remains may help to resolve this question.

Hominin material from 102c

The 102c deposit is a very small (~2 L) volume of sediment enclosed within a dissolution cavity in the cave wall. Only one morphologically identifiable hominin specimen has been recovered from this area. U.W. 102c-589 is a fragment of left mandibular corpus with worn LM1 and LM2 in situ (Figure 31). These teeth have less occlusal wear than those of the LES1 mandible, but are morphologically very similar. The mandibular corpus is broken irregularly at the alveoli and the base of the mandible is not present. Anteriorly, it is broken at the mesial M1 root; posteriorly, it is broken at the mesial alveolus for the M3. The root of the ascending ramus is preserved and becomes independent at approximately the midpoint of M2. Corpus breadth at M2 is approximately the anatomical value at 19.8 mm; the broken corpus does not permit this measurement elsewhere.

The morphology of the mandible and tooth crowns is similar to that of the mandibular remains of H. naledi from the Dinaledi Chamber. The size and preserved morphology of the mandibular corpus and root of the ascending ramus are very similar to that of the DH1 holotype of H. naledi. The morphology and wear stage of the U.W. 102 c-589 LM1are nearly identical to those of the U.W. 101–297 RM1 crown from the Dinaledi sample, and the LM2 is very similar in morphology to the U.W. 101–284 LM2 from Dinaledi (Figure 31). Neither of the U.W. 102 c-589 teeth exhibit supernumerary cusps, and both have simple crowns with a Y-5 cusp pattern without crenulation or complexity, similar to the Dinaledi teeth. The areas represented by the cusps appear similar to those in the Dinaledi molars, as do the crown heights. The relatively small size of the mandible and molars rule out attribution to Au. africanus or P. robustus, and the crown morphology rules out attribution to H. erectus or H. habilis. This mandible is entirely consistent with H. naledi.

The U.W. 102 c-589 mandible clearly duplicates the LES1 mandible, thereby demonstrating the presence of a second adult individual in the Lesedi Chamber as a whole. Nevertheless, it is more difficult to determine whether the U.W. 102 c-589 individual also contributed a femur to 102a, accounting for the evidence of two adult individuals in that deposit. The 102c deposit is separated by a distance of approximately 12 m from the 102a assemblage. While this distance does not rule out the occurrence of the remains of a single individual in both locations, the context does not provide any reason for an assumption that they are the same.

Taphonomy

The general preservation of the Lesedi Chamber hominin material resembles that of the skeletal assemblage from the Dinaledi Chamber (Dirks et al., 2015). The Lesedi skeletal material has a surface coloration that ranges from light grey to red-brown, and internal structures or cortex at fresh break points are colored pale buff to off-white, contrasting with unbroken adjacent surfaces. The remains present no evidence of calcite crystal formation. Specific comments on preservation have been included with the specimen descriptions above, and taphonomic observations on each specimen are summarized in Supplementary file 5.

The Lesedi skeletal assemblage exhibits varying degrees of post-mortem damage. Most specimens are fragmented or broken to some degree, with areas of cortical bone removal or abrasion (Supplementary file 5). All fractures observed in the assemblage are consistent with post-mortem (dry bone) failure (Supplementary file 5), and there are no spiral or incomplete fractures indicative of green or wet bone (L’Abbé et al., 2015; Symes et al., 2014). Fractures in the assemblage include transverse or right-angled breaks on the shafts of long bones, showing block-comminution between major breaks and step-fractures following the longitudinal grain of the long bone, which are distinct from cracking or crazing resulting from weathering (Symes et al., 2014).

The Lesedi remains display no evidence of sub-aerial weathering processes (sensuBehrensmeyer, 1978; see also Lyman and Fox, 1989 and Junod and Pokines, 2014, indicating that the dry bones were not subject to surface processes before deposition in the cave environment. Sub-aerial weathering is primarily characterized by both cracking and delamination. Within the Lesedi assemblage, there is some evidence of surface cracking, but it generally does not penetrate deep into the cortex. No indications of the secondary features of weathering, such as delamination, deep patination, bleaching or cortical exfoliation, were observed in any of the bone fragments from Lesedi, suggesting that the bones were not affected by surface exposure (Supplementary file 5). A comparison with human bone derived from forensic or sealed archaeological contexts (Figure 32) suggests that the cracking and fracture patterns observed in the Lesedi assemblage can be explained most parsimoniously by the effects of the burial environment (Pokines, 2014), and were exacerbated in specimens where fluctuations in moisture content caused swelling and shrinkage of the cortical structure (Conard et al., 2008; Dirks et al., 2016; Dirks et al., 2015).

Surface cracking and pitting in Lesedi Chamber material.

Top: right corpus and ramus of LES1 mandible prior to reconstruction, showing patterns of cracking consistent with the effects of sediment loading and wetting during the burial process and during skeletal decomposition. This pattern of taphonomic alteration is superficially similar to sub-aerial weathering processes, but is independent of surface exposure and occurs in both deep- and shallow-buried deposits. Middle: forensic known-history case for comparison. This specimen was recovered from a deep known-history inhumation. The fleshed body was deposited at a depth of 1.5 metres and recovered after a 30-year burial period. Note the similarities in surface texture, and superficial cracking, which follows the biomechanical stress lines (grain) of the bone. Bottom: U.W. 102a-010 acromial fragment showing surface modification with cortical pitting and punctate marks. Note that many of these marks (circled in yellow) penetrate pre-existing layers of manganese oxy-hydroxide deposited on the bone surface; the damage was therefore produced inside the Lesedi Chamber on bones that were already covered in coatings of manganese mineral.

As with the Dinaledi material, some of the Lesedi Chamber remains are stained by iron oxides and manganese oxy-hydroxide (Dirks et al., 2015; Randolph-Quinney et al., 2016). This staining primarily occurs as diffuse spots or mats of mineral, some of which cover and encapsulate the fractured ends of long bones, indicating a complex post-mortem history of mineral deposition. However, we have observed no mineral tide marks upon the Lesedi Chamber skeletal material which, unlike material from the Dinaledi Chamber, provides us with no information about the former position of skeletal remains relative to the sediment–air interface. Some of the Lesedi material exhibits minor pitting, striations, grooves, scratches, or gouges. Striations and grooves are consistent with abrasion marks, as defined by D’Errico and Villa (1997) and Fisher (1995). Some of the elements have a palimpsest of taphonomic traces, with mineral deposition preceding invasive surface modification or fracturing (Figure 32). The pitting that is present on the Lesedi material shows that the modifying agents (abiotic or biotic) penetrated already-altered bone, suggesting that damage occurred on bone surfaces that were already covered in coatings of manganese and iron oxide (Randolph-Quinney et al., 2016). Generally, the pattern of pitting and stripping is similar in composition and gross morphology to patterns observed in the Dinaledi Chamber assemblage, which were attributed to gastropod and other invertebrate activity (Dirks et al., 2015, 2016; Randolph-Quinney et al., 2016), although these must be studied in more detail to be certain.

Overall, the gross taphonomic signature of the hominin remains in the Lesedi Chamber appears consistent with sub-surface deposition with limited post-depositional dispersal. Particularly in the U.W. 102a locality, this is evidenced by the presence of articulated remains, the proximity of cranial and postcranial remains, and the recovery of small elements such as teeth and carpals. The bone surface condition, as well as the absence of other markers of transport and secondary modification, are generally consistent with sub-surface skeletal decomposition (Carter and Tibbett, 2008; Carter et al., 2007). At present, we find no supporting evidence for sub-aerial weathering or post-mortem exposure outside of the cave environment (Hill, 1976; Junod and Pokines, 2014; Lyman and Fox, 1989; Tappen and Peske, 1970). Nor are there signs of carnivore or scavenger modification (Pokines, 2013), water transport (Behrensmeyer, 1988; Evans, 2013), or peri-mortem trauma such as may be expected in a natural death-trap scenario (L’Abbé et al., 2015; Symes et al., 2014).

Faunal material

In addition to the hominin skeletal material, some faunal remains have been recovered from the Lesedi Chamber. Over 80 faunal elements or fragments were collected from U.W. 102a. U.W. 102b yielded 23 specimens of fauna, while a single rodent tooth was recovered from U.W. 102c. In-depth analyses of the faunal material are ongoing, and comprehensive descriptions are in preparation. We provide here a preliminary list of the taxa identified for reference (Table 3).

Table 3

Mammal species recorded in the Lesedi Chamber. Several specimens from the classes Aves, Amphibia and Reptilia were also recovered, but individual counts and taxonomic identifications are pending further examination.

The Lesedi faunal assemblage includes micromammal, small to mid-size mammal, and non-mammalian remains. With respect to the micromammals (prey body mass <500 g), 5 genera of rodents and 1 genus of shrew were identified out of 28 craniodental specimens (21 MNI). There are also potentially two additional murine genera and one soricid genus present in the assemblage, although lower-level identification is not possible at this time. Interestingly, all of the non-hominin fauna are of relatively small species. The largest mammalian specimens come from dental material attributed to Canis aff. C. familiaris. The size range of this material is outside the range of modern C. mesomelas but the morphology is definitively not Lycaon (Hartstone-Rose et al., 2010; Wayne, 1986). The felid material is also small, falling in the size range of the African wildcat. None of these individuals is likely to have exceeded 10–15 kg (Kingdon, 2015) and the rest of the assemblage consists almost entirely of animals smaller than 3 kg, including four specimens from the family Herpestidae. Aside from a single lagomorph specimen, the macro-mammalian material comes exclusively from the order Carnivora, a situation that is unusual in the fossil record (Werdelin and Sanders, 2010).

We do not presently know whether some or all of these faunal remains may be contemporaneous with any of the hominin fossil material. Faunal remains have been recovered both on the surface and also from within sediments near hominin remains. However, the Lesedi Chamber is not a completely isolated environment, and sediment deposits are currently eroding from their original depositional contexts, with evidence for slumping and reworking in the chamber. Therefore, we cannot yet comment on the relative timing of deposition of the hominin and faunal material. Additional tests, including attempts to date both hominin and faunal elements directly, will help us answer these questions and to relate the faunal material to the chronological and environmental context of H. naledi in the Lesedi Chamber.

Discussion

The hominin material from all three excavation contexts in the Lesedi Chamber can be clearly attributed to H. naledi, and no diagnostic material in this chamber represents any other hominin taxon. This confirms that a second chamber within the Rising Star cave system, in a distinct depositional context isolated from the Dinaledi Chamber, also holds the skeletal remains of H. naledi.

As in the Dinaledi Chamber, both adult and immature individuals are commingled in the Lesedi Chamber. When the fossils recovered from the 102a, 102b, and 102c localities are considered in aggregate, duplication of elements and age-at-death indicators combine to produce a MNI of three: two adults and one immature individual. However, the presence of material in three spatially separated localities within the chamber leads us to hypothesize that the current collection more probably represents additional individuals. The adult mandibular fragment in 102c is separated from the adult femora in 102a by more than 10 m, and the presence of this fragment in 102c, with an opening 1.3 m above the present cave floor, suggests that the sedimentary deposits may once have been much more voluminous. In light of the situation, we view it as likely that the 102c mandibular fragment represents an additional adult individual beyond what may be two individuals in 102a. The 102b deposit is separated by less distance from 102a, and the data do not yet provide a clear answer as to whether or not the juvenile remains in both areas could represent a single individual. Considering the spatial context, we hypothesize that four individuals may be represented: two adults and one immature individual in 102a and 102b; and one adult in 102c. Further excavation may test this hypothesis.

The Lesedi Chamber sample extends our knowledge of H. naledi in several ways. The complete U.W. 102a-021 clavicle confirms the morphological assessment of fragmentary clavicles from the Dinaledi Chamber (Feuerriegel et al., 2017). The U.W. 102a-036 and U.W. 102a-151 T10 and T11 vertebrae duplicate the anatomy observed in the Dinaledi material (Williams et al., 2017), while additional vertebrae add information on the lower vertebral column. The U.W. 102a-250 first rib is more complete than any example from the Dinaledi Chamber, but presents similar anatomy (Williams et al., 2017). U.W. 102b-438 and its associated teeth present an additional immature mandibular specimen that adds to the developmental series of mandibles and immature dentitions from the Dinaledi Chamber. Comparative study of these elements is underway.

The relative completeness of the LES1 cranium allows us to examine cranial length and the nasal aperture for the first time in H. naledi, in part confirming the interpretation of partial crania and isolated cranial elements from the Dinaledi Chamber. This specimen shows a relatively short and tall cranium and a moderate-sized nasal aperture. This specimen expands the range of endocranial volume (ECV) known for H. naledi, which now extends from approximately 460 ml to approximately 610 ml. The maximum value for H. naledi is now somewhat above the maximum ECV observed for australopith species, including Au. afarensis, Au. africanus, P. robustus, and P. boisei (Table 4; Figure 33). No crania attributed to H. habilis, H. rudolfensis, or H. erectus have ECVs as small as the 460 ml estimated for DH3, but the larger H. naledi specimens do overlap with the smaller end of the reported values for H. habilis and H. erectus. The single specimen of H. floresiensis with an estimate of endocranial volume, LB1, is smaller than any specimen of H. naledi. The addition of the LES1 cranium now brings the range of observed ECVs in H. naledi into overlap with two specimens of H. erectus (D2700 and D4500 from Dmanisi; Table 4, Figure 33).

Endocranial volumes of hominin species.

With the addition of LES1 to the sample, the range of endocranial volume in H. naledi is extended slightly beyond the range represented in the Dinaledi Chamber. This range overlaps with two specimens of H. erectus, and LES1 is larger than the largest Au. africanus or Au. afarensis specimens. Data and sources are listed in Table 4.

The hominin material from the Lesedi Chamber remains undated. The Dinaledi Chamber hominin material appears to have been deposited sometime between 236 ka and 335 ka (Dirks et al., 2017). The Dinaledi hominin sample is morphologically very uniform, and variations in many metric characters in that sample is less than those in local populations of modern humans (Berger et al., 2015). Such morphological uniformity suggests that the Dinaledi Chamber does not represent successive biologically diverse populations sampled over tens of thousands of years or longer, known as ‘time-averaging’, but instead may sample a single biological population. The Lesedi Chamber H. naledi sample adds very little to the morphological variability of the Dinaledi Chamber sample, and most measurements of cranial, dental, and postcranial elements fall within the existing range known from that chamber. The nonmetric traits observed on cranial and postcranial elements from the Lesedi Chamber are nearly all duplicated in the Dinaledi Chamber sample (Supplementary file 1; Figures 34 and 35). It is therefore reasonable to hypothesize that the Lesedi Chamber may sample the same biological population as the Dinaledi Chamber. This hypothesis will be tested with further geological information, including attempts to apply direct dating to the hominin material directly. If the two hominin assemblages represent diverse geological ages, or if either assemblage was deposited over a geologically long time interval, they would demonstrate a remarkable stasis of H. naledi metric and morphological characters across time.

Selected cranial trait observations in H. naledi and other species.

A subset of observations of cranial traits reported in Supplementary file 1 that vary among species attributed to Homo. This list omits traits that are present in only one species of Homo or for which nearly all species exhibit more than one state. Here, the character state observed in H. naledi, including both Dinaledi Chamber and Lesedi Chamber material, is reported on the left. Character states for other species are reported in terms of whether they share the same state as H. naledi. Some traits that are shared with H. naledi may be interpreted as shared derived traits, based on their absence from Au. afarensis and Au. africanus, but some species of Homo also share primitive traits with H. naledi that may also be found in the australopiths. The pattern of shared morphological characters among these species and H. naledi is complex, and there is no consistent anatomical grouping of the characters shared with any given species. H. naledi shares more characters with H. erectus and H. habilis than with other species, and behind them, with Au. sediba and archaic and modern humans. H. erectus is variable for a large number of traits also found in H. naledi. The fact that variability is noted in H. erectus, Neandertals and modern humans for these traits is partially a function of the large samples available for these groups. It is probable that a larger sample of other species would likewise encompass greater variability. Any phylogenetic tree of these species would reveal a high degree of homoplasy for these cranial and mandibular traits.

Postcranial traits in H. naledi compared to those in other hominin species.

Here, a subset of features of the postcranial skeleton that distinguish H. naledi from other species are summarized in comparison to these traits in other hominin species with substantial postcranial evidence. These features include some that H. naledi shares with Au. afarensis, some that H. naledi shares with modern humans or Neandertals, and some that are unique or shared with even more distantly related species such as Ardipithecus (not shown). These traits constitute a mosaic that distinguishes H. naledi clearly from other species of Homo. Many of the traits that are notable in the Dinaledi Chamber sample are also represented in the Lesedi Chamber material.

The emphasis of this study has been to test the hypothesis that the newly discovered Lesedi skeletal material represents H. naledi. Based upon this diagnosis, the morphology of H. naledi (including the Lesedi material) across the skeleton has implications for its relationship to other Plio-Pleistocene hominins (Figures 34 and 35). Most of the anatomical features across the skeleton of H. naledi are known from multiple specimens, many of which have now been replicated in two assemblages (Figure 35). Phylogenetic analysis of the Dinaledi hominin assemblage has shown that the mosaic of features in the H. naledi cranium and dentition does not provide unambiguous or clear evidence of where the species should be placed in the phylogeny of Homo (Figure 34; Dembo et al., 2016). We briefly consider here how the overall pattern of morphological and temporal evidence relates to the possible affinities of H. naledi with other hominins.

Lateral cranial comparison of H. naledi crania to crania of other hominin species.

H. naledi crania, DH1, LES1, and DH3 are in the center row. All crania are oriented as near as possible to the Frankfort plane, delineated by the light gray lines in the background of the figure. Compared to other hominin genera, including Australopithecus and Paranthropus, fossil Homo is often recognized by cranial and dental features such as a more vertical face profile, a reduced postcanine dentition, larger endocranial volume, a higher frontal, and a true supraorbital torus. Au. africanus (Sts 5, top left) represents the ancestral hominin condition lacking these traits. The other crania in the top two rows vary substantially in these features. LB1 has a vertical face, reduced dentition, and high, rounded frontal, but has comparatively small endocranial volume. KNM-ER 1470 has a large volume, a high frontal, and a more vertical face profile, but also is inferred to have a large postcanine dentition and has no true supraorbital torus. MH1 (Au. sediba) has a small volume, but shares features with Homo that include the less sloping face profile, a supraorbital torus, and reduced postcanine dentition. O.H. 24 has a low, sloping frontal, and a concave facial profile, but a true supraorbital torus and reduced postcanine teeth. This variability among species that are interpreted as ‘primitive’ Homo, such as H. habilis and H. floresiensis, and Homo-like australopiths makes it difficult to delineate the genus Homo (Wood and Collard, 1999; Dembo et al., 2016). H. erectus is also highly variable. It includes several crania with endocranial volumes below 700 ml, including KNM-ER 42700 and D2282, but also many larger crania, here represented by Sangiran 17 and Zhoukoudian L2 (ZKD L2). Specimens attributed to H. erectus tend to share a series of traits first noted in Asian H. erectus samples, including a long, low cranial profile, thick cranial bone, sagittal keeling, prominent supraorbital, angular, and occipital tori, a sharply angled occiput, and a postbregmatic depression. The smallest H. erectus crania share most of these features, with a low cranial profile, angled occiput and postbregmatic depression visible here in D2282. But these features do vary substantially and are less evident in the immature KNM-ER 42700. The H. naledi crania are similar to KNM-ER 1470 in having a transversely flat clivus contour, but all are smaller, with a much smaller palate and with very different frontal morphology. Like O.H. 24 and KNM-ER 1813, the H. naledi crania have relatively thin cranial bone and a thin and projecting supraorbital torus. But H. naledi manifests a different clivus shape, a projecting nasal spine, a greater cranial height, sagittal keeling and an angular torus. The H. naledi crania bear little resemblance to LB1, differing in face profile, size, and their larger postcanine dentitions. Known African Homo specimens from the later Middle Pleistocene other than H. naledi, such as the Kabwe skull (pictured), contrast strongly with H. naledi in cranial size and morphology. The Omo 2 skull, one of the earliest known modern human crania at approximately 196,000 years (McDougall et al., 2005), is vastly larger and very different from any H. naledi specimen, despite being near the same geological age. In this figure, O.H. 24, KNM-ER 1470, LB1, KNM-ER 42700, ZKD L2, and Omo 2 are represented by casts. Images have been adjusted to a common scale by maximum cranial length, or by glabella-bregma length where maximum length is not available. Photos of Sangiran 17 and D2282 are courtesy of Milford Wolpoff.

Homo floresiensis

The late Middle Pleistocene geological age of H. naledi, when considered together with its small endocranial volume, prompt comparisons with H. floresiensis. Skeletal remains of H. floresiensis are known from ~100–60-ka-old sediments at Liang Bua, Flores (Brown et al., 2004; Sutikna et al., 2016), and possibly also in Mata Menge, Flores sediments from the early Middle Pleistocene (van den Bergh et al., 2016; Brumm et al., 2016). The features shared by H. naledi and H. floresiensis are nearly all inferred to be primitive features shared with australopiths and/or in some cases with early Homo (Figures 35 and 36). For most features of the skeleton where H. naledi exhibits derived morphology, including aspects of the foot and hand, H. floresiensis exhibits morphology thought to be primitive within hominins (Harcourt-Smith et al., 2015; Kivell et al., 2015; Tocheri et al., 2007; Jungers et al., 2009a; Orr et al., 2013). All known H. floresiensis long bones are small, reflecting small stature and mass (Jungers et al., 2009b; Larson et al., 2009; Grabowski et al., 2015), and none approach the much larger size, particularly the taller stature, manifested in adult specimens of H. naledi. The mandibles of H. floresiensis are relatively robust, even for their small size,(Brown and Maeda, 2009; Daegling et al., 2014) and in this sense, are comparable to the robust mandibles of H. naledi, though the two species differ in symphyseal morphology (Laird et al., 2017). The dentition of H. floresiensis displays a unique combination of primitive and derived characters (Kaifu et al., 2015), which are different from the combination found in H. naledi. Homo floresiensis canines and premolars display a combination of features that are primitive for hominins (Kaifu et al., 2015), while H. naledi mandibular canines and third premolars have a uniquely derived form. The H. floresiensis molars exhibit derived proportions and some other features similar to those of modern humans, which may reflect the extremely shortened molar crowns, particularly of the first molars (Kaifu et al., 2015). By contrast, H. naledi has primitive proportions of the molars and occlusal morphology that is broadly primitive within Homo, although simplified in complexity. Shape analyses also place the cranium of H. floresiensis (LB1) far from any H. naledi cranial specimen (Schroeder et al., 2017). These differences in anatomy may reflect a distant phylogenetic relationship between the two species, although these data do not clearly resolve where on the Homo phylogeny either species should be placed. Some phylogenetic evidence suggests that the H. floresiensis branch preceded the node linking H. erectus and modern humans (Argue et al., 2009; Dembo et al., 2015). Cranial and dental evidence does not resolve whether H. naledi may also have branched early in the evolution of Homo, or whether it may instead be a sister taxon to modern and archaic humans (Dembo et al., 2016). No data that are available at present answer whether either or both of these lineages may have retained small EVC from an ancestry among the earliest members of Homo, or whether their smaller brain sizes may have evolved secondarily from larger-brained ancestors. Together, they establish that diverse hominin lineages with varying brain and body sizes existed during the Middle Pleistocene, suggesting the influence of ecological factors that promoted diversity during the Pleistocene evolution of humans and great apes (Berger et al., 2017; Tocheri et al., 2011, 2016; Dunn et al., 2014).

Homo erectus

H. naledi shares many derived cranial and dental characters with H. erectus (Figures 34 and 36; Dembo et al., 2016; Laird et al., 2017), and Dmanisi specimens of H. erectus are among the closest in multivariate shape to H. naledi crania (Schroeder et al., 2017). H. naledi overlaps with H. erectus in long bone lengths, inferred stature, and estimated body mass (Figure 28; Berger et al., 2015). To the extent that the H. naledi postcranial skeleton is different from material attributed to H. erectus, it is mostly because H. naledi manifests primitive traits that are not otherwise seen in Homo, or because H. naledi manifests traits not otherwise seen in hominins (Figure 35). H. naledi also shares several derived postcranial features with archaic and modern humans, but a lack of postcranial evidence for these parts of the H. erectus skeleton has made it impossible to determine whether H. erectus may also have shared these derived features (Figure 35). With respect to the cranium and dentition, nearly all of the nonmetric traits shared by H. naledi and H. erectus are also shared with Au. sediba, H. habilis, or both (Supplementary file 1; Figure 34). H. naledi and H. erectus share at least three derived nonmetric features of the skull that are not also found in Au. sediba or H. habilis: an angular torus, sagittal keeling, and an anteriorly projecting nasal spine. But each of these three traits can also be found in some archaic or modern humans. H. naledi also possesses some cranial and dental traits not seen in any specimens of H. erectus; these include both primitive traits shared with Au. afarensis, Au. africanus or Au. sediba and derived traits shared either with H. rudolfensis or with archaic and modern humans. Even though H. naledi crania are most similar in shape to the smallest H. erectus crania from Dmanisi (Schroeder et al., 2017), they are distinct from the Dmanisi sample in numerous aspects of cranial, dental, and postcranial morphology (Berger et al., 2015; Laird et al., 2017; Marchi et al., 2017; Feuerriegel et al., 2017; Rightmire et al., 2017), and Bayesian analysis of cranial and dental morphology provides strong evidence against the hypothesis of a sister taxon relationship for these samples (Dembo et al., 2016). In summary, no traits link H. naledi exclusively or specifically with H. erectus, and many traits distinguish the two. The evidence is not sufficient to say whether H. naledi may have evolved from an earlier population that resembled H. erectus, or whether earlier fossils representing the H. naledi lineage may already have been found and until now attributed to H. erectus (Berger et al., 2017).

Australopithecus sediba, Homo habilis, and Homo rudolfensis

Fossil samples from Malapa, Olduvai Gorge, and the Lake Turkana area have been attributed to lineages often thought to represent some of the earliest species of Homo or their near relatives among the australopiths. H. naledi shares many derived cranial and mandibular features with Au. sediba and H. habilis, although most of these are also shared with H. erectus (Supplementary file 1; Figures 34 and 35). Compared to these other species, H. naledi shares many fewer cranial and dental features with H. rudolfensis, except for its relatively flat and squared nasoalveolar clivus. Phylogenetic analysis does not reject the hypothesis of a sister taxon relationship between H. naledi and Au. sediba or H. habilis (Dembo et al., 2016). However, in comparison to both Au. sediba and H. habilis, H. naledi is derived and similar to modern humans and Neandertals in several aspects of hand and wrist morphology (Kivell et al., 2015). It is also derived in its foot morphology in comparison to both MH2 of Au. sediba and the O.H. 8 foot usually attributed to H. habilis (Harcourt-Smith et al., 2015). H. naledi also lacks the derived configuration of the Au. sediba ilium (Figure 35). H. naledi further shares a number of derived cranial characters with H. erectus and with archaic or modern humans as discussed above (Supplementary file 1, Figure 34). Whatever the relationship of these species, their evolution must have involved homoplasy of many features and the evidence does not yet make it clear how they are connected. If any one of these species were a possible ancestor of H. naledi, the branch leading to the Dinaledi sample of H. naledi would approach 1.5 Ma or longer in evolutionary time. With abundant opportunity for adaptive and nonadaptive evolution of the H. naledi lineage over this time, it would be very hard to distinguish a long branch connecting it to Au. sediba or H. habilis from a somewhat longer branch connecting it to the very base of Homo.

Conclusions

The excavation of the Lesedi Chamber has added to our knowledge of the biology of H. naledi and has confirmed the presence of this species in a second depositional context. The skeletal material described here derives from a very small and limited excavation, and the total sediment volume of the chamber has not yet been sampled sufficiently to estimate the abundance of hominin-bearing deposits or the relationship of faunal and hominin species. Further resolution of how the material was originally deposited must await more detailed sedimentological analysis and more excavation work.

The relative completeness of the morphological evidence from H. naledi has not resolved its phylogenetic placement within the genus Homo (Dembo et al., 2016). The morphological evidence from the Lesedi Chamber hominin material reinforces the observations made on the basis of the Dinaledi hominin sample. In particular, the more complete LES1 cranium and the more fragmented cranial remains from multiple individuals already known for H. naledi share an almost identical pattern of derived features with other hominin species (Laird et al., 2017). The discovery of H. naledi within the Dinaledi Chamber documented a pattern of anatomy that had not been anticipated by anthropologists on the basis of earlier fossil discoveries. Learning how H. naledi connects to other fossil evidence of human origins may require more unexpected discoveries.

Materials and methods

Excavation

Formal excavations began in the Lesedi Chamber in May 2014, after initial surface and ex situ material had been recovered. Like the Dinaledi Chamber, the access route to the Lesedi Chamber is very restricted. Additionally, the excavation area available in the Lesedi Chamber is considerably more confined than that in the Dinaledi Chamber. As a result, protocols followed those used in the Dinaledi Chamber (Dirks et al., 2015), with a few exceptions. Specifically, attempts to use some of the surface-scanning methods applied in the Dinaledi Chamber (Kruger et al., 2016) failed due to the limited working distances of the scanner, the convoluted surfaces, and the poor contrast of the surrounding dolomite. However, high-resolution laser scan data have been acquired for the Lesedi Chamber and will form the basis of future spatial work. Consequently, documentation of the excavations and provenience of the material was conducted using traditional archaeological methods, including written descriptions, photography and drawings. Excavations were conducted in tandem with geological mapping and with sedimentologic and taphonomic analyses of the site.

For excavations in U.W. 102a, the area was divided into 20–40 cm sections that were based on the contours of the sloped surface and the width of the tunnel at that point. Sections were excavated in 2–5 cm levels. In some areas where few specimens were being recovered, levels were expanded to 10 cm.

In the U.W. 102b area, excavations began on the surface of the sediment deposit in which the first material was recovered, and proceeded in 2–5 cm levels until the chert layer on which the sediment had accumulated was reached. When this area was exhausted, excavations moved along the chert shelf, removing sediments from the surface, to the chert, in 20 cm horizontal sections. A sediment pocket above the fossil deposit (on Chert 3) was also excavated to determine whether material had trickled down from above. Preliminary excavations were also begun on the antechamber floor below the primary fossil deposit.

Owing to the confines of the dolomite recess in which the hominin material was found, U.W.102c was not divided into sections. However, it was also excavated in 2–5 cm levels, from the top of the sediment accumulation to the chert shelf at its base.

For all three areas, all sediments were collected for every section and level separately. Each bag of back dirt was labeled, removed from the cave and dry screened to recover small elements, fragments and microfaunal remains. All sediments were retained and are currently stored at the University of the Witwatersrand’s Evolutionary Studies Institute.

Comparative samples

Taxonomic identification of the Lesedi Chamber hominin material depended on a series of systematic comparisons to other hominin species. Many of these observations were carried out on the original fossil specimens by the authors; some have relied upon observations taken from research-grade casts of fossil specimens available at the University of the Witwatersrand and elsewhere, while in some cases, observations were only available from the literature. The fossil comparative samples employed in this study are essentially the same as those described in Berger et al. (2015), with the addition of the Dinaledi Chamber sample of H. naledi (Berger et al., 2015; Kivell et al., 2015; Marchi et al., 2017; Feuerriegel et al., 2017; Laird et al., 2017; Williams et al., 2017; Zipfel and Berger, 2009). The gross morphological appearance and dental dimensions of the remains immediately made it clear that they were inconsistent with Paranthropus, and with Australopithecus afarensis, Australopithecus africanus, or Australopithecus garhi, and so we focused our comparisons upon Homo and Australopithecus sediba. The composition of samples of other hominin species is as follows, largely repeated from Berger et al. (2015).

Australopithecus sediba. The partial skeletons MH1 and MH2 from Malapa, South Africa were included in this study on the basis of examination of the original specimens by the authors.

Homo habilis. Samples from Olduvai Gorge, East Lake Turkana, the Omo Shungura sequence, Hadar, and Sterkfontein were considered within the hypodigm of H. habilis for this study. Original Olduvai Gorge and East Lake Turkana fossils were examined first-hand, whereas for the Omo and Hadar materials, we relied on our original observations on casts and originals and published reports (Tobias, 1991; Boaz et al., 1977; Kimbel et al., 1997). As in the initial announcement of H. naledi (Berger et al., 2015), in this paper we adopt a conservative approach that follows a more conventional hypodigm, thereby encompassing a maximum amount of variation in this taxon; for a more detailed discussion of the probable hypodigms of early Homo species, see de Ruiter et al., 2017. We therefore include the following fossils in the hypodigm of H. habilis: A.L. 666–1, KNM-ER 1478, KNM-ER 1501, KNM-ER 1502, KNM-ER 1805, KNM-ER 1813, KNM-ER 3735, O.H. 4, O.H. 6, O.H. 7, O.H. 8, O.H. 13, O.H. 15, O.H. 16, O.H. 21, O.H. 24, O.H. 27, O.H. 31, O.H. 35, O.H. 37, O.H. 39, O.H. 42, O.H. 44, O.H. 45, O.H. 62, OMO-L894-1, and Stw 53.

Homo rudolfensis. Samples from Olduvai Gorge, East Lake Turkana, and Lake Malawi were considered as part of the hypodigm of H. rudolfensis for this study. The East Lake Turkana fossils available prior to 2010 were examined first-hand, while for the Olduvai and Lake Malawi fossils and for KNM-ER 60000, 62000, and 62003, we relied on original observations of fossils and casts as well as published reports (Blumenschine et al., 2003; Schrenk et al., 1993; Leakey et al., 2012). As above, and in the initial announcement of H. naledi (Berger et al., 2015), in this paper we adopt a conservative approach that follows a more conventional hypodigm, thereby encompassing a maximum amount of variation in this taxon; for a more detailed discussion of the probable hypodigms of early Homo species, see de Ruiter et al. (2017). We include the following fossils in the hypodigm of H. rudolfensis: KNM-ER 819, KNM-ER 1470, KNM-ER 1482, KNM-ER 1483, KNM-ER 1590, KNM-ER 1801, KNM-ER 1802, KNM-ER 3732, KNM-ER 3891, KNM-ER 60000, KNM-ER 62000, KNM-ER 62003, O.H. 65, and UR 501.

A large number of postcranial specimens have been collected from the Turkana Basin and appear consistent with the anatomical range otherwise found in Homo, and inconsistent with known samples of Australopithecus and Paranthropus from elsewhere. These include KNM-ER 1472, KNM-ER 1481, KNM-ER 3228, KNM-ER 737, KNM-ER 5881 (Ward et al., 2015), and others.

Specimens from the latest Lower Pleistocene and Middle Pleistocene of Europe and Africa that cannot be attributed to H. erectus were also included in the comparisons in this study. These include fossils that have been attributed to H. heidelbergensis, H. rhodesiensis, ‘archaic H. sapiens’ or ‘evolved H. erectus’ by a variety of other authors. Specimens include KNM-ES 11693, Arago 2, Arago 13, Arago 21, Atapuerca 1, Atapuerca 2, Atapuerca 4, Atapuerca 5, Atapuerca 6, Cave of Hearths, Ceprano, SAM-PQ-EH1, Kabwe, Mauer, Ndutu, Salé, Petralona, Reilingen-Schwetzingen, and Steinheim. We also included Neandertal samples from Krapina, Vindija, La Chapelle-aux-Saints, La Ferrassie, Monte Circeo, Saccopastore, and Feldhofer.

Endocranial volume estimation

The LES1 ECV was estimated virtually using 3D surface scans of the reconstructed partial cranium. These methods were similar to those performed on the previously published Dinaledi H. naledi crania (Berger et al., 2015). The LES1 partial cranium was scanned using a NextEngine 3D Scanner and associated ScanStudio HD Pro software. Two 360-degree scans were collected using 16 divisions and 1000 dpi with the cranium in different orientations in order to capture the maximum ectocranial and endocranial surfaces. The two 360-degree scans were then merged and exported as a .ply file. The .ply file was opened in GeoMagic Studio, converted to a point cloud, and re-wrapped to minimize the number of edges in the model (created from the individual surface scans). The LES1 virtual model was then duplicated and mirrored, and the mirror-image (right portion) was aligned with the original model (left portion) using both the Manual and Global Registration functions. In doing this, the program uses an iterative process to find the greatest congruency between the region of overlap in the two models, minimizing deviations. Convergence was detected after 20 iterations, with an average deviation of 0.47 mm and a standard deviation of 0.43 mm. Some deviation is expected given the natural anatomical asymmetry and refitting of the fragments. A deviation map illustrates that areas with the highest deviation were fairly localized (Figure 37). We inspected the mirror image in comparison to the preserved but not refitted fragments that represent portions of the right parietal and right temporal bones of LES1, finding that they are similar in size and curvature. The LES1 original images and mirror-image were then merged.

LES1 model congruency.

Congruency between the original LES1 3D scan and an aligned mirror-image. Scale bar = 2 cm. (A) Frontal view of a 3D scan of the original LES1 specimen (brown) aligned with the mirror-image (grey), illustrating congruency between overlapping regions. (B) Deviation map of the internal view of the frontal region. Deviation scale bar in mm.

The endocranial surface was then isolated by manually selecting the surfaces and creating a new model (Figure 38). Fragment edges were deleted and small holes in the model were filled using the ‘Fill by Curvature’ function. Gaps in the model remained in the posterior parietal, occipital, and cranial base regions. In order to compute a volume, the model must be completely closed; thus, these regions were carefully filled using either the ‘Fill by Curvature’ or ‘Flat Filling’ functions depending on the regions. This procedure was carefully monitored and the approximated surfaces were modified as necessary to ensure that they were congruent with the endocranial surfaces present. The volume of the closed endocranial model was then computed in GeoMagic Studio.

Previous research suggests that using a model cranial base from another hominin taxon does not significantly alter virtual estimate results (Berger et al., 2015); however, given the uniformity in the cranial base reconstruction of the endocranial model presented here (e.g., the lack of consideration for sella turcica, etc.), the current estimate may be a slight overestimate. Holloway (personal communication) found that by manually constructing a cranial base, ECV estimates for the previously published DH1/DH2 and DH3/DH4 H. naledi composite endocasts decreased by 5 ml (0.9% and 1.1%, respectively).

Taphonomy

The hominin assemblage from the Lesedi Chamber was analysed using the taphonomic protocols and methods applied to the U.W. 101 Dinaledi fossils, and detailed in Dirks et al. (2015): 22–24 and 32–33. Specimens were viewed macroscopically, and fragments >50 mm diameter were imaged on all surfaces using a Canon 70D DSLR fitted with a Canon EF-S 60mm f2.8 macro lens and ring-flash. Criteria for scoring taphonomic observations are detailed in Supplementary file 5. Additional taphonomic analyses are underway and will be described in future publications.

Faunal identifications

The taxonomic classification of the micromammal remains follows that of Wilson and Reeder, 2005, using published descriptions and images (Avery, 2007; Coetzee, 1972; Davis, 1965; De Graaff, 1981; Meester and Setzer, 1971; Reppening, 1967; Skinner and Chimimba, 2005), as well as comparisons with a photographic database of southern African rodents from various museum collections. As genus is the lowest taxonomic level at which most material can be identified accurately (Reed, 2005, (2007); Reed and Geraads, 2012), specimens were identified to this level or higher. Macrovertebrate remains were also identified using published reference guides (Walker, 1985) and visual comparisons with mammalian collections at the University of the Witwatersrand. Wherever possible, specimens were attributed to species. In cases where this was not possible, the next highest taxonomic level was used. Identification of the non-mammalian remains was limited to the level of class or order, pending more detailed analyses.

Access to material

All fossil material from the Lesedi Chamber is available for study by researchers upon application to the Evolutionary Studies Institute at the University of the Witwatersrand where the material is curated. Three-dimensional surface renderings and other digital data are available from the MorphoSource digital repository (http://morphosource.org).

Decision letter

George H Perry

Reviewing Editor; Pennsylvania State University, United States

In the interests of transparency, eLife includes the editorial decision letter and accompanying author responses. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.

Thank you for submitting your article "New fossil remains of Homo naledi from the Lesedi Chamber, South Africa" for consideration by eLife. Your article has been reviewed by three peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Ian Baldwin as the Senior Editor. One of the three reviewers, Chris Stringer, has agreed to share his name. The other reviewers remain anonymous.

The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you prepare a revised submission.

Following the initial report of the new hominin taxon Homo naledi from the Dinaledi Chamber of the Rising Star cave system in South Africa, published in eLife in 2015, this paper describes and details a second set of Homo naledi fossils from an additional chamber of the Rising Star system, Lesedi. The discovery is extraordinary. While the reviews of the submitted manuscript are largely complimentary, there are two substantial issues that need to be addressed prior to publication (see the reviews for specific details):

1) The overall view from the reviewers is that well-designed comparative figure(s), illustrating how Homo naledi morphology differs from that of other hominins, would greatly aid readers as they examined the new data and results as they consider the descriptions and conclusions. This analysis should specifically include smaller-bodied hominins from Africa, as well as Homo floresiensis. To some extent, addressing this issue may be aided by clear citation to previous morphological descriptions and comparisons from your group's recent publications; however, the present manuscript should be as interpretable and valuable on its own as possible. That is, since new material is being presented and discussed in the larger hominin fossil context, it would be useful and is important to have a richer visual comparative guide as part of this manuscript.

2) Taphonomic observations of the individual hominin specimens should be provided as part of this paper on a bone-by-bone basis, even if there is some overlap with the other paper under consideration.

In addition to the two largest issues mentioned above, I am choosing to take the unusual step (for eLife) of providing the full reviews as part of the decision letters for each of the co-submitted papers, for two reasons. First is the interconnectedness among the multiple papers submitted, which is reflected in the reviews (as some reviewers participated in the review of multiple papers). Seeing the more direct reader reactions to each paper in the context of others should be helpful (and should be taken into account) as you consider the larger revision process for the entire group of papers. The comments provided by the reviewers identify issues additional to the two listed above that must be addressed. Note that one reviewer also provided specific comments (using tracked changes) in the attached document.

We will likely ask reviewers to evaluate the revised manuscript before considering it for acceptance.

Reviewer #1:

This is a fairly straightforward paper describing the new H. naledi remains from another chamber in the Rising Star cave system. I do think that it would be helpful if they included taphonomic observations of the individual hominin specimens. I know that the overall taphonomy of the hominin bones are discussed in an accompanying paper by Elliott et al., but perhaps it would make sense for the authors to include it here in more detail on a bone-by-bone basis. It is hard to tell from pictures, but it does appear that some of the specimens may be weathered, for example, the mandibular fragment shown in Figure 21 and many limb elements appear to have damaged or missing epiphyses. There hasn't been much done on weathering patterns in caves, but generally speaking, weathering is associated with exposure. In a protected environment like a cave chamber, I would not expect much or any weathering at all. The authors attribute the breakages observed to sediment loading (was the cave filled with sediments at one point?), inadvertent human activity, and matrix effects (from the accompanying paper by Elliott et al.). But I am not sure that the damage seen on the epiphyses (Figures 15–18) is consistent with those factors. With weathering on the bone, it would suggest some exposure to sun, wind, and other abrasion agents. I think that taphonomy of the hominin specimens should be something that is addressed in some detail as it impacts interpretations of how the bones got into the cave system in the first place.

Reviewer #2:

Overall: This is an interesting paper providing straightforward descriptions of the new hominin fossils from the Lesedi Chamber from the Rising Star system that expand the hypodigm of the interesting Homo naledi assemblage. The new cranium (along with the partial skeleton, hopefully associated) represents an extraordinary finding. I look forward to see this paper published to see the reaction of the scientific community, as well as the criticisms from other colleagues.

The main problem with this paper, however, is that in its current form there is not a single comparative figure where one can actually see how H. naledi differs from other fossils. Hawks et al., are forcing the readers to believe all the statements about how different this taxon is from previously known hominins. Well-designed comparative figures pointing out the distinctive morphologies of H. naledi would strengthen the arguments of this study and make it a great addition to the literature.

In relation to the above, why there are not qualitatively and quantitatively comparisons with other small Homo from Africa (KNM-ER 42700, KNM-ER 5881) and especially H. floresiensis? Aside from the wrist, it is like the hobbit does not exist at all to these authors.

Endocranial size:

There are several individuals from Dmanisi, and KNM-ER 42700, which show that some Homo erectus exhibit an almost equally small endocranial volume as Homo naledi. Although it is true that none is smaller than 460 ml (DH3), this needs to be discussed more. Again, and importantly: LB1 exhibits an endocranial volume of 417 cm3 and there is no mention to it, nor the implications of it. On the other hand, the wrist bones of H. floresiensis are compared to those of H. naledi.

Figures:

Could the authors remove all of the extra black background and focus on the fossils? It would be a much better use of the figures if we could actually see the fossil morphologies discussed in the papers. Also, please provide figures of all the described material (e.g., ulna, hand bones).

Other minor comments to consider:

- Regarding the pillars on the femoral neck 'This configuration is not seen in other hominin species.' The authors do not show a clear figure of this (not in the past papers, either). It seems like this must be figured here. I would actually say that, to make a compelling case, they need to show this morphology in H. naledi alongside a large sample of other hominins, particularly Pleistocene Homo femora.

- The discussion of number of individuals confusing. Lines 510-512 propose a single adult present, but then lines 651-653 say two adults.

- Line 681, The authors should define specifically what is the hypodigm that they refer as to 'Homo erectus sensu lato'

- Figure 10 (top) shows some Lesedi Mc4's metrics. Since claims are made that shaft and head robusticity is distinct from modern humans, it would be good to have pictures of the actual specimens to compare. Also, please notice that for the relative midshaft breadth the Lesedi Mc4 specimens fall well within the modern human range.

Also, the formatting of the boxplot axes is odd (overlaying the title of the axes). The font size of the x-axis is too small.

- Figure 10 (bottom), could the authors provide the% of variance explain in each axis? Also, the y-axis is stretched relative to the x-axis.

Reviewer #3:

In my view this paper should be suitable for publication after minor editing.

The references for all four papers need work for consistency of formatting, journal abbreviations, accents etc.

"The molar size gradient in the mandible is M1 < M2 < M3, and in the maxilla is M1 < M3 < M2, both identical to that observed in the Dinaledi Chamber sample of H. naledi." Wasn't M1 < M2 < M3 the pattern in the Dinaledi maxillary dentitions too?

"We refer to this putative skeletal individual as "Neo ", which is the Setswana word meaning "a gift"." How does this assist the analysis? Names like this are better left for the media and popular coverage?

"The hominin material from the Lesedi Chamber remains undated as this would require physical destruction of the specimens prior to their description." Techniques using laser ablation are minimally destructive and could have been attempted by now?

Reviewer #3 Minor Comments:

I have added suggested edits to a text version of the paper, which I attach.

[Further changes were requested before acceptance.]

Thank you for resubmitting your work entitled "New fossil remains of Homo naledi from the Lesedi Chamber, South Africa" for further consideration at eLife. Your revised article has been evaluated by a Reviewing Editor and five peer reviewers representing the intersection of the two previously submitted manuscripts from which this current version was created.

The reviewers were complimentary about the progress made on the manuscript in this revised version, but they note several outstanding larger issues, as well as a relatively long list of smaller or technical items, that must be addressed.

Major Issues:

1) The manuscript provides insufficient support for the hypotheses that there has been no post-depositional dispersal and that the faunal elements entered the chamber after the hominins. Either (A) sufficient, convincing evidence needs to be provided, or (B) this section needs to be removed along with the conclusions related to deposition. There are multiple detailed reviewer comments provided below that pertain to this topic, which all together should help to illustrate the strong consensus view among reviewers on these points.

At this point, we strongly suggest that the authors take approach (B), with a simplified presentation of these data and a straightforward statement that issues regarding the timing and method of deposition and post-depositional dispersal are the subjects of ongoing research to be fully addressed later.

2) The reviewers felt that the revisions to address the previous decision letter's request for comparative figures illustrating that the morphology of H. naledi is distinct from previously recognized hominin taxa, were not sufficient. Since the conclusions in this manuscript are drawing support from the new Lesedi material and not simply or only referencing prior published comparisons, the overall reviewer and editorial consensus is that additional visual comparisons (i.e., that more fully compare the discussed Lesedi material to the original H. naledi material, and both to the morphology of other hominin taxa), are necessary.

Detailed Comments:

1) Regarding the chamber itself and the deposits within it, it is still not quite clear if the deposits that contain skeletal material represent the only deposits in this chamber that do contain such material, or if they are just the ones that were investigated (or, in fact, just the ones that were investigated that do contain such material). Part of this confusion arises from the fact that the authors never really say why they decided to pick those three particular parts of the chamber as they did, nor how much estimated deposit (hominin-bearing or otherwise) might remain. I am sure this will be of great interest to most readers, as the authors seem to imply that more skeletal material from these same individuals may be recovered in the future.

2) Lines 894-897: "sub-surface deposition with limited post-depositional dispersal" May be the case for U.W. 102a, but the preservation of only small cranial fragments and partial mandible from 102b, and solely a mandibular fragment from 102c suggests there was post depositional dispersal. Unless the authors are claiming the cranial fragments were originally deposited as isolated fragments, and then not dispersed afterwards. If an entire cranium decomposed, most cranial bones should be present unless there was significant post-depositional dispersal or significant pre-depositional dispersal (which is not discussed here).

3) Lines 930-941: The authors propose the hypothesis that the faunal remains entered the chamber well after the deposition of the hominins, but do not present convincing or conclusive evidence that they are NOT contemporaneous, nor that the hominids material was not deposited in the same manner as the other faunal remains (contemporaneous or not). I know that this was transferred from the Lesedi geology paper, but the authors do not present "evidence for slumping and reworking of the sediments above the hominin layers" and claim there is a "lack of clear stratigraphic association", but do not present information on the stratigraphic association (or stratigraphy period) to determine if the interpretation is supported by evidence. In short, what precludes the hominid material from being deposited by the same method (and therefore associated) as the other faunal remains? Similarly, if the immature hominin remains in 102b could be the result of slumping from around 102a (in Discussion), why couldn't the same situation be ascribed to the other fauna, arguing for the exact same pattern of deposition (and possible association). I would suggest that the entire paragraph be removed except for the first sentence, which could be added to the first paragraph of the "Faunal material" and include these issues of association with the "ongoing" research to be addressed later. Otherwise, as is, the authors are presenting interpretations without presenting the data/information behind said interpretations.

4) The authors still do not provide evidence for their hypotheses that there has been no post-depositional dispersal and that the faunal elements entered after the hominins. If the taphonomic factors are the same for all 3 chambers, which is what they suggest, then one would expect that hominin element representation would be fairly similar, but instead, there are articulated and associated specimens in 102a, but only isolated cranial fragments from 102b and c. The fact that there aren't more elements must suggest that there was some post-depositional disturbance. Otherwise, where are they? The authors suggest that the hominin deposit was much more extensive at one point (960-961), the natural question to that is, what happened? What post-depositional process occurred to substantially decrease the hominin material? I won't go into detail regarding my thoughts on the issue of contemporaneity of the hominin and faunal specimens, but I think that the authors need to provide the evidence or remove the section.

5) Line 935-941: These are all valuable observations, but they lead to an impression that the authors are pushing a depositional scenario that removes the timing of hominin deposition from the faunal remains without sufficient evidence to do so. I recommend either softening these assertions or giving additional weight to other possibilities. For example, they mention that there are "differences in preservation" of faunal and hominin remains but do not specify what those are. The fact that all faunal remains are all carnivores, indeed, suggests that perhaps small carnivores entered the cave system, became disoriented, and ended up in the chamber because they were following the scent of decomposing tissue. Without comparisons via direct radiometric or relative ages/geochemical signatures on the faunal and hominin remains, this section must remain more speculative than is made out to be. There are some very simple (albeit minimally destructive) tests that could be carried out that would definitively resolve this.

6) My main concern in the previous version of this work was the lack of comparisons with other hominins (both analytical and graphical). Besides taphonomic details, in the revised version of their manuscript, Hawks et al provide extensive tables comparing cranial, mandibular and dental characters of the Lesedi fossils with those previously attributed to H. naledi as well as other hominin species. The authors now also incorporated a comparative figure (their Figure 10) the LES1 skull with selected hominins in lateral view. Although I applaud these incorporations, I still miss comparisons of the rest of the fossils. Claims are made that H. naledi (including the Lesedi material) is clearly distinct from previously recognized hominin taxa, and that these distinctive morphologies are spread throughout the body. However, there are not comparative figures showing the distinct morphology alongside other hominins. To be fair, the existing postcranial material of early Homo is very scant (and some not attributed to any specific taxon), and it would be very difficult to make the case that H. naledi is really distinct based on its postcrania. Thus, I would appreciate it if the authors made the effort to recognize this limitation (at the moment there is no way to really tell whether or not H. naledi is just a late H. habilis). Based on the metrics reported by the authors, only two dimensions of the maxillary M1 seems distinct from other early Homo, and this is based on small samples of the latter.

7) Only the combination of 18 variables of two wrist bones together in a single multi-group discriminant analysis shows that Lesedi and Dinaledi are distinct (Figure 16). However, I wonder if these fossils were left ungrouped in this analysis or whether were they included as their own OTU. If it is the latter case, the null hypothesis is that this analysis will show how distinct these specimens are, rather than to which other taxa they resemble. More importantly, even for the case of the wrist bones (supposedly very distinct), they are not morphological comparisons with other fossils (the same applies for all the other postcranial and dental material). Why are the authors hesitant to show morphological comparisons with other hominin materials? Again, the readers should be able to evaluate the distinctiveness of the new fossils by themselves. I understand that full morphometric comparisons can follow in future studies, but I believe this paper is not complete without more graphical comparisons.

8) I think that the authors have sufficiently addressed my comment regarding the appearance of weathering on the bones. I am very glad that they included the detailed table on the taphonomy of the hominids; however, as is, it does raise questions about how they scored some of the taphonomic variables. For example, how did they score heavy vs. patchy staining, what is excellent, good, fair, and poor preservation? Also, the table needs to be reformatted. It is very difficult to read it in its current format.

9) Line 170: Use of "in situ" implies that there is good evidence the skeletal material has not been moved substantially from its place of deposition. It seems like reworking and spreading out of material is fairly common inside this chamber (for example, reference to the "apron" of material), so I am unsure "in situ" is the appropriate term without some qualification. My preference would be to describe the assemblage as minimally reworked, as evidenced by some articulated elements and refitting fragments/individuals, but to avoid use of "in situ" unless it is very clearly the original place of deposition.

10) Location of chamber: All the information about the various parts of the cave system (knee-breaker, pinch and punch, etc.) should be either left out or included on the Figure 2 diagram.

11) Based on various reviewer comments, a small clarification is needed for consistency between the abstract and later in the text, on the minimum number of individuals present. When hypothesizing that there may be at least four individuals, first restate that the confirmed minimum is three.

Author response

Editorial comments:

Comparative analyses and figures.

We have reorganized the descriptions to emphasize the comparative anatomy as a separate section where appropriate with each anatomical element. The key similarities and differences between H. naledi and other species are now highlighted in each of these sections, with specific reference to fossil specimens in other species. For the LES1 cranium, this section is newly added and summarizes the key comparisons with other species with reference to the more descriptive and detailed analyses of the Dinaledi hominin sample published by Laird et al. (2017) and Schroeder et al. (2017). We have added one large comparative figure that presents visual comparisons between LES1 and key specimens of other species of Homo. We have also included many references to the descriptive papers that provide more detail and comparative figures including Dinaledi fossil remains of H. naledi.

Taphonomy.

We have ensured that each anatomical description includes a brief statement about conditions of its preservation, surface appearance, and any other details that affect the interpretation of the anatomy. In addition, we have added the new Table 6, which presents observational data pertinent to taphonomy for each bone specimen. This should conform to the instruction for a bone-by-bone treatment of taphonomic observations. The text has brought the section on general taphonomy from the manuscript by Elliott et al. This has been augmented to discuss in some detail whether the surface condition of the bones is consistent with subaerial weathering or moisture cycles within a buried environment, as requested by reviewers. We have added a new Figure 29 that shows a direct visual comparison of surface cracking on a Lesedi Chamber specimen paired with a comparable specimen from a controlled burial.

Context.

At the suggestion of the editors, we have taken three additional sections from the paper by Elliott et al. and added them to this paper with appropriate edits in response to reviewer comments. These include the sections describing the name of the Lesedi Chamber, the location of the chamber within the Rising Star cave system with detail about the three excavation areas, and the list of faunal species recovered in the chamber. These aspects are the essential ones for understanding the location of the hominin remains and any possible geological associations. The paper by Elliott et al. includes substantial detail concerning the sediment facies, formation of the deposits and other matters that do not directly impinge on the identification or taxonomic assessment of the hominin remains, and we leave those for a resubmission of that work to another journal. The author lists of the two papers have been merged with appropriate weight on contributions.

Reviewer comments:

Weathering: The surface condition of the bones have been described in some detail both bone-by-bone and in a general taphonomy section. The conditions under which cracking and some abrasion have occurred are compatible with a long underground burial, and surface modifications were made after deposition of manganese on the surfaces.

H. floresiensis: We have added text with explicit comparisons to LB1 and other H. floresiensis remains where appropriate throughout the paper. We have also updated the endocranial volume as reflected by the newer estimations by Kubo et al. 2013. Qualitative comparisons with other hominin species are presented in Table 2 and should now be clear in text for the postcranial skeleton.

Black backgrounds: We appreciate the reviewer’s comment concerning background color. When deciding on photo backgrounds, we have to weigh many issues including the range of end-users of these open-access photos, for whom a dark background is commonly requested for use in lectures, courses and comparisons with other fossil hominins on black backgrounds. We have worked to make each image as legible and true to the color of the specimen as possible. We are also providing freely downloadable surface models of the fossils for readers who want a better ability to inspect the orientations and outlines of specimens.

Ulna and metacarpal figures have been added.

Femoral neck: This morphology has been pictured by Marchi et al. (2017) in two figures, which were probably not yet available at the time of the review. As these have now been published, we have cited that paper here.

Number of adults: We have clarified this in text.

Hand and wrist figures: We have changed these plots in several ways to enhance their readability. The text now reports more detail about the canonical variates analysis, and Table 5 now presents all correlations between variables and CV1 and CV2.

Molar size gradient: We have expanded this paragraph to clarify that the maxillary molar size gradient, which was not described in earlier publications, is not the same as the mandibular molar size gradient in H. naledi.

Laser ablation: The accompanying paper by Dirks et al. expresses our protocols for geological sampling and destructive sampling for dating purposes. While laser ablation for U-series dating can allow a rapid assessment of whether material has substantial antiquity, the method is limited to determining a minimum age based on uranium uptake. In the case of the Dinaledi tooth samples, the direct U-Th minimum ages are much lower than the dates as estimated by ESR. Proceeding with only the laser ablation U-Th approach would have yielded very misleading results. In our case we do not pursue any destructive sampling of material without an integrated plan for combination of methods, including biomolecule sampling in addition to stable isotope and radioisotope sampling. We hope that this process maximizes information and confidence in the end results, and it is also consistent with our understanding of the heritage regulations that apply to this work.

[Further changes were requested before acceptance.]

We have addressed the two editorial directives as follows:

a. We followed the advice to simplify all aspects related to deposition and site formation to a bare minimum, so that we are presenting data with no unsupported conclusions about these matters. To be clear, we completely agree with the reviewers that post-depositional dispersal of some material has happened, and that we do not know the timing of entry of faunal material, and we did not intend to give any other impression.

b. We have included 6 new figures (7, 10, 11, 12, 28, and 36) that feature comparative photographs of Lesedi Chamber fossil material, examples from the Dinaledi Chamber, and selected fossil specimens from other sites, as appropriate. These illustrate the cranium, mandible, dentition, and femur, which join the existing comparative figures that present data on tooth size, vertebral morphology and hand and wrist morphology. We have also included 2 new figures (34 and 35) that present visual summaries of the anatomical evidence for similarity and difference with other species in a phylogenetic context for cranial and mandibular, and postcranial features, respectively. One more new figure (33) presents a visual comparison of endocranial volume data, and Figure 13 has been changed to add comparative data on maxillary and mandibular canine size in H. naledi and other species. We would love to add even more specimens in some of the comparative figures, but high-quality images or casts of many fossils are not available to include. We think the new figures strike an appropriate balance of illustrating well-known fossils, for which many researchers have casts in their reference or teaching collections, in combination with fossils from both the Dinaledi and Lesedi Chamber assemblages. We have prioritized including comparative images of Dmanisi specimens as these have previously been compared to the cranial and mandibular anatomy of H. naledi, and these specimens are not part of most researchers’ cast collections. In addition to these new figures, we have added 4 paragraphs to the conclusion discussing how combined morphological and temporal evidence address the relationship of H. naledi to (1) archaic and modern humans, (2) H. floresiensis, (3) H. erectus, and (4) Au. sediba, H. habilis, and H. rudolfensis.

We have also taken the opportunity to move large tables into Supplementary Files, which we think will make them easier to read. Each of these has been edited and formatted for readability.

Our changes responding to each of the reviewer comments are numbered here as in the decision letter (rather than re-iterating the full comment).

1. Why did we dig where we did? We appreciate this comment because many of the other questions are easily answered when the very limited scope of the excavation is understood. We have revised our discussion on pages 5 and 6, of the location of fossils in the chamber, to make clear that the total excavation to date involves an extremely small and limited sampling of the chamber’s contents, and our investigation of the three areas followed discovery of fossils on the surface, not any systematic sampling. A clear description of the very small excavation volumes (< 200 L in total, only <20 L for 102b and 2 L for 102c) probably answer other reviewer questions or place them better into context.

2. The question about postdepositional dispersal of material is well taken. We have addressed this in the text by (1) clearly stating our working hypothesis that extensive sediment removal has happened during the history of the chamber, as well as reinforcing that postdepositional processes may have dispersed material, (2) removing any parts that appear to assume anything about the formation or subsequent history of the deposits.

3. Faunal material: We agree with the reviewer here who notes that we do not know whether the fauna are contemporary with the hominins, and that is exactly what we hope to convey. Our impression from the reviewer comments is that including alternate hypotheses for entry may confuse matters by making it appear that we are pushing for non-association. Accordingly, we have edited the text to remove any speculative statements so that we do not seem to be pushing any hypothesis and are strictly limiting to the data.

4. Why is there a discrepancy in element representation between 102a, 102b and 102c? We think that this question is now answered by our description of the excavation areas, where we are clear that the 102b and 102c excavations each comprise only a few liters of sediment. The 102c deposit, for example, could not contain very much material.

5. This comment also concerns the timing of faunal deposition. We think that the edits to this section, which now only say that we do not know whether the faunal remains and hominins are contemporary, will address this comment.

6. Comparative figures. We have added the 8 new figures and comparative text to Discussion as noted above. Figure 35 helps to address some of the concerns with lack of postcranial evidence in other species. The figure clearly notes all instances where data are missing from other species, and delineates the Dinaledi Chamber evidence from the evidence that is present in both chambers.

7. Wrist bones discriminant function. This comment seems to have misunderstood the text. The analysis of the scaphoid and capitate morphology is a canonical variates analysis (CVA) and discriminant function analysis is one special case of canonical correlation, we have not carried out a discriminant function analysis here. It is not our aim to assign the fossil specimens to groups based on their anatomy, but to graphically show how the fossil specimens compare to the extant taxa and each other, specifically in terms of their scaphoid and capitate anatomy. We have examined the results of discriminant function analysis and they are fundamentally identical; that is, whether Homo naledi (or the other fossil specimens) is included as its own a priori group or as a posteriori unknown specimens, the CVA results are essentially identical. Just to avoid any confusion, we have added a title to that CVA plot in addition to the description of the CVA analysis in text and the figure caption. We have moved the details of the analysis from a table into Supplementary file 4.

8. Taphonomy table. We have revised this table so that it is more legible on the page. We have moved this to Supplementary file 5. This supplementary file also now includes a new table with scoring criteria for each observation and detailed references for all observations made on the preservation of the bone material.

9. In situ. This term causes a lot of confusion as it is used differently by archaeologists, taphonomists, and geologists. We have removed it except where it refers to the instance of articulated remains.

10. Description of chamber: We have omitted all nonessential details concerning the cave system and names of locations other than the Lesedi and Dinaledi Chambers.

11. MNI: We have edited the text in accord with the suggestion here to reflect both the “confirmed minimum” and what we view as the more likely alternative in light of the spatial context.

Article and author information

Author details

John Hawks

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Department of Anthropology, University of Wisconsin, Madison, United States

Contribution

JH, assisted in project conception and administration, developed methodology, supervised analyses, investigated morphological and contextual information, carried out statistical analyses, curated data, created visualizations, wrote the original draft and edited the paper

Contribution

MMS, investigated dental material, carried out formal analyses, and wrote part of the manuscript

Competing interests

The authors declare that no competing interests exist.

Matthew W Tocheri

Department of Anthropology, Lakehead University, Thunder Bay, Canada

Human Origins Program, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, United States

Contribution

MWT, investigated hand and wrist material, carried out formal analyses, and wrote part of the manuscript

Competing interests

The authors declare that no competing interests exist.

Caroline VanSickle

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Department of Anthropology, University of Wisconsin, Madison, United States

Department of Anthropology, Bryn Mawr College, Bryn Mawr, United States

Contribution

CV, investigated pelvic material, carried out formal analyses, and wrote part of the manuscript

Competing interests

The authors declare that no competing interests exist.

Christopher S Walker

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Department of Evolutionary Anthropology, Duke University, Durham, United States

Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, United States

Contribution

CSW, investigated lower limb material, carried out formal analyses, and wrote part of the manuscript

Competing interests

The authors declare that no competing interests exist.

Timothy L Campbell

Department of Anthropology, Texas A&M University, College Station, United States

Contribution

TLC, investigated faunal material, carried out formal analyses, and wrote part of the manuscript

Competing interests

The authors declare that no competing interests exist.

Brian Kuhn

Department of Geology, University of Johannesburg, Johannesburg, South Africa

Contribution

BK, investigated faunal material, carried out formal analyses, and wrote part of the manuscript

Competing interests

The authors declare that no competing interests exist.

Ashley Kruger

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa

Contribution

AK, analyzed spatial data and support for fieldwork

Competing interests

The authors declare that no competing interests exist.

Steven Tucker

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

ST, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Alia Gurtov

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Department of Anthropology, University of Wisconsin, Madison, United States

Contribution

AG, carried out fieldwork in the Lesedi Chamber, recovered and recorded hominin fossil material

Competing interests

The authors declare that no competing interests exist.

Nompumelelo Hlophe

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

NH, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Rick Hunter

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

RH, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Hannah Morris

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Department of Forestry and Natural Resources, University of Georgia, Athens, United States

Contribution

HM, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Becca Peixotto

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Department of Anthropology, American University, Washington, United States

Contribution

BP, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Maropeng Ramalepa

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

MR, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Dirk van Rooyen

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

DvR, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Mathabela Tsikoane

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

MT, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Pedro Boshoff

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

PB, carried out fieldwork in the Lesedi Chamber, investigated contextual data and assisted in design of excavation methodology

Competing interests

The authors declare that no competing interests exist.

Paul HGM Dirks

Geosciences, College of Science and Engineering, James Cook University, Townsville, Australia

Contribution

PHGMD, assisted with the conception of the project, developed methodology, investigated stratigraphic and contextual information, supervised contextual analyses, assisted in creating visualizations and wrote part of the manuscript

Competing interests

Lee R Berger

Evolutionary Studies Institute, University of the Witwatersrand, Wits, South Africa

Contribution

LRB, led the conception and administration of the project, developed field and laboratory methodology, carried out formal analyses, investigated morphological and contextual information, wrote parts of the manuscript

Texas A and M College of Liberal Arts (Seed Grant Program)

National Geographic Society

National Research Foundation

Gauteng Provincial Government

Palaeontological Scientific Trust

Lyda Hill Foundation

Lee R Berger

Fulbright Scholar Program

John Hawks

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

The authors would like to thank the many funding agencies that supported various aspects of this work. In particular, the authors would like to thank the National Geographic Society, the South African National Research Foundation and the Gauteng Provincial Government for particularly significant funding of the discovery, recovery and analysis of this material. Other funding agencies include and the Palaeontological Scientific Trust, the Texas A&M College of Liberal Arts Seed Grant Program, the Lyda Hill Foundation, the Wisconsin Alumni Research Foundation, the Vilas Trust, and the Fulbright Scholar Program. Further support was provided by ARC (DP140104282: PHGMD, ER, HHW). We wish to thank the Jacobs Family, and later the Lee R. Berger Foundation for Exploration, for access to the site, and the South African Heritage Resource Agency and Cradle of Humankind UNESCO World Heritage Site Management Authority for issuing the various permits required for this work, including the excavation permit (PermitID: 952). We would also like to thank the University of the Witwatersrand and the Evolutionary Studies Institute, as well as the South African National Centre of Excellence in PalaeoSciences, for curating the material and for hosting the authors while they were studying the material.

Reviewing Editor

George H Perry, Reviewing Editor, Pennsylvania State University, United States

Further reading

New ages for flowstone, sediments and fossil bones from the Dinaledi Chamber are presented. We combined optically stimulated luminescence dating of sediments with U-Th and palaeomagnetic analyses of flowstones to establish that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity (sub-unit 3b), interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested by varying the assumed levels of 222Rn loss in the encasing sediments: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils. By combining the US-ESR maximum age estimate obtained from the teeth, with the U-Th age for the oldest flowstone overlying Homo naledi fossils, we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology.

Homo naledi is a previously-unknown species of extinct hominin discovered within the Dinaledi Chamber of the Rising Star cave system, Cradle of Humankind, South Africa. This species is characterized by body mass and stature similar to small-bodied human populations but a small endocranial volume similar to australopiths. Cranial morphology of H. naledi is unique, but most similar to early Homo species including Homo erectus, Homo habilis or Homo rudolfensis. While primitive, the dentition is generally small and simple in occlusal morphology. H. naledi has humanlike manipulatory adaptations of the hand and wrist. It also exhibits a humanlike foot and lower limb. These humanlike aspects are contrasted in the postcrania with a more primitive or australopith-like trunk, shoulder, pelvis and proximal femur. Representing at least 15 individuals with most skeletal elements repeated multiple times, this is the largest assemblage of a single species of hominins yet discovered in Africa.

We describe the physical context of the Dinaledi Chamber within the Rising Star cave, South Africa, which contains the fossils of Homo naledi. Approximately 1550 specimens of hominin remains have been recovered from at least 15 individuals, representing a small portion of the total fossil content. Macro-vertebrate fossils are exclusively H. naledi, and occur within clay-rich sediments derived from in situ weathering, and exogenous clay and silt, which entered the chamber through fractures that prevented passage of coarser-grained material. The chamber was always in the dark zone, and not accessible to non-hominins. Bone taphonomy indicates that hominin individuals reached the chamber complete, with disarticulation occurring during/after deposition. Hominins accumulated over time as older laminated mudstone units and sediment along the cave floor were eroded. Preliminary evidence is consistent with deliberate body disposal in a single location, by a hominin species other than Homo sapiens, at an as-yet unknown date.

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